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This paper describes a method for determining an atomic model of a protein complex using moderate-resolution cryoEM data and distance predictions from deep learning., Cryo-electron microscopy of protein complexes often leads to moderate resolution maps (4–8 Å), with visible secondary-structure elements but poorly resolved loops, making model building challenging. In the absence of high-resolution structures of homologues, only coarse-grained structural features are typically inferred from these maps, and it is often impossible to assign specific regions of density to individual protein subunits. This paper describes a new method for overcoming these difficulties that integrates predicted residue distance distributions from a deep-learned convolutional neural network, computational protein folding using Rosetta, and automated EM-map-guided complex assembly. We apply this method to a 4.6 Å resolution cryoEM map of Fanconi Anemia core complex (FAcc), an E3 ubiquitin ligase required for DNA interstrand crosslink repair, which was previously challenging to interpret as it comprises 6557 residues, only 1897 of which are covered by homology models. In the published model built from this map, only 387 residues could be assigned to the specific subunits with confidence. By building and placing into density 42 deep-learning-guided models containing 4795 residues not included in the previously published structure, we are able to determine an almost-complete atomic model of FAcc, in which 5182 of the 6557 residues were placed. The resulting model is consistent with previously published biochemical data, and facilitates interpretation of disease-related mutational data. We anticipate that our approach will be broadly useful for cryoEM structure determination of large complexes containing many subunits for which there are no homologues of known structure.

Based on the molecular-dynamics simulation platform Amber, a refinement algorithm has been developed to obtain structural models of protein crystals in the form of a fully hydrated unit cell. These models typically yield better R free values and MolProbity scores compared with the PDB-deposited or Phenix-refined coordinates. The new algorithm has a favorable radius of convergence, is simple to use and is fast., A procedure has been developed for the refinement of crystallographic protein structures based on the biomolecular simulation program Amber. The procedure constructs a model representing a crystal unit cell, which generally contains multiple protein molecules and is fully hydrated with TIP3P water. Periodic boundary conditions are applied to the cell in order to emulate the crystal lattice. The refinement is conducted in the form of a specially designed short molecular-dynamics run controlled by the Amber ff14SB force field and the maximum-likelihood potential that encodes the structure-factor-based restraints. The new Amber-based refinement procedure has been tested on a set of 84 protein structures. In most cases, the new procedure led to appreciably lower R free values compared with those reported in the original PDB depositions or obtained by means of the industry-standard phenix.refine program. In particular, the new method has the edge in refining low-accuracy scrambled models. It has also been successful in refining a number of molecular-replacement models, including one with an r.m.s.d. of 2.15 Å. In addition, Amber-refined structures consistently show superior MolProbity scores. The new approach offers a highly realistic representation of protein–protein interactions in the crystal, as well as of protein–water interactions. It also offers a realistic representation of protein crystal dynamics (akin to ensemble-refinement schemes). Importantly, the method fully utilizes the information from the available diffraction data, while relying on state-of-the-art molecular-dynamics modeling to assist with those elements of the structure that do not diffract well (for example mobile loops or side chains). Finally, it should be noted that the protocol employs no tunable parameters, and the calculations can be conducted in a matter of several hours on desktop computers equipped with graphical processing units or using a designated web service.

The ambient-pressure phase α of C4H2N5Cl transforms under 0.18 GPa to a higher-symmetry phase α′, but its high-pressure recrystallization below 0.20 GPa leads to a stochastic hydrate while above 0.20 GPa recrystallization leads to a new phase, β., Partial hydration of organic compounds can be achieved by high-pressure crystallization. This has been demonstrated for the high-nitro­gen-content compound 6-chloro-1,2,3,4-tetrazolo[1,5-b]pyridazine (C4H2N5Cl), which becomes partly hydrated by isochoric crystallizations below 0.15 GPa. This hydrate, C4H2N5Cl·xH2O, is isostructural with the ambient-pressure phase α of C4H2N5Cl, but the crystal volume is somewhat larger than that of the anhydrate. At 0.20 GPa, the α-C4H2N5Cl anhydrate phase transforms abruptly into a new higher-symmetry phase, α′; the transformation is clearly visible due to a strong contraction of the crystals. The hydrate α-C4H2N5Cl·xH2O can also be isothermally compressed up to 0.30 GPa before transforming to the α′-C4H2N5Cl·xH2O phase. The isochoric recrystallization of C4H2N5Cl above 0.18 GPa yields a new anhydrous phase β, which, on releasing pressure, transforms back to the α phase below 0.15 GPa. The structural transition from the α to the β phase is destructive for the single crystal and involves a large volume drop and significant elongation of all the shortest intermolecular distances which are the CH⋯N and CH⋯Cl hydrogen bonds, as well as the N⋯N contacts. The α-to-α′ phase transition increases the crystal symmetry in the subgroup relation; however, there are no structural nor symmetry relations between phases α and β.

The 2.22 Å crystal structure of a multi-drug exporter, CmABCB1, was determined by the LCP-SFX method using the XFEL beamline at SACLA. The lipid bilayer-embedded structure revealed new insights about the substrate transport mechanism of CmABCB1., CmABCB1 is a Cyanidioschyzon merolae homolog of human ABCB1, a well known ATP-binding cassette (ABC) transporter responsible for multi-drug resistance in various cancers. Three-dimensional structures of ABCB1 homologs have revealed the snapshots of inward- and outward-facing states of the transporters in action. However, sufficient information to establish the sequential movements of the open–close cycles of the alternating-access model is still lacking. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers has proven its worth in determining novel structures and recording sequential conformational changes of proteins at room temperature, especially for medically important membrane proteins, but it has never been applied to ABC transporters. In this study, 7.7 mono­acyl­glycerol with cholesterol as the host lipid was used and obtained well diffracting microcrystals of the 130 kDa CmABCB1 dimer. Successful SFX experiments were performed by adjusting the viscosity of the crystal suspension of the sponge phase with hy­droxy­propyl methyl­cellulose and using the high-viscosity sample injector for data collection at the SACLA beamline. An outward-facing structure of CmABCB1 at a maximum resolution of 2.22 Å is reported, determined by SFX experiments with crystals formed in the lipidic cubic phase (LCP-SFX), which has never been applied to ABC transporters. In the type I crystal, CmABCB1 dimers interact with adjacent molecules via not only the nucleotide-binding domains but also the transmembrane domains (TMDs); such an interaction was not observed in the previous type II crystal. Although most parts of the structure are similar to those in the previous type II structure, the substrate-exit region of the TMD adopts a different configuration in the type I structure. This difference between the two types of structures reflects the flexibility of the substrate-exit region of CmABCB1, which might be essential for the smooth release of various substrates from the transporter.

A series of halogenated compounds with motion-capable moieties were designed and synthesized, and they exhibit different π-stacking arrangements. The thermal expansion behaviors are influenced by crystal packing, halogen-bond strength and pedal motion ability., A series of aromatic organic molecules functionalized with different halogen atoms (I/ Br), motion-capable groups (olefin, azo or imine) and molecular length were designed and synthesized. The molecules self-assemble in the solid state through halogen bonding and exhibit molecular packing sustained by either herringbone or face-to-face π-stacking, two common motifs in organic semiconductor molecules. Interestingly, dynamic pedal motion is only achieved in solids with herringbone packing. On average, solids with herringbone packing exhibit larger thermal expansion within the halogen-bonded sheets due to motion occurrence and molecular twisting, whereas molecules with face-to-face π-stacking do not undergo motion or twisting. Thermal expansion along the π-stacked direction is surprisingly similar, but slightly larger for the face-to-face π-stacked solids due to larger changes in π-stacking distances with temperature changes. The results speak to the importance of crystal packing and intermolecular interaction strength when designing aromatic-based solids for organic electronics applications.

When biomedical crises strike, structural biologists worldwide respond by determining the structures of relevant proteins and their complexes, resulting in an avalanche of data that can be overwhelming without a resource designed to classify, annotate and validate them. An advanced information system is necessary to extract and infer knowledge from a deluge of uncurated and disjointed data and publications., As part of the global mobilization to combat the present pandemic, almost 100 000 COVID-19-related papers have been published and nearly a thousand models of macromolecules encoded by SARS-CoV-2 have been deposited in the Protein Data Bank within less than a year. The avalanche of new structural data has given rise to multiple resources dedicated to assessing the correctness and quality of structural data and models. Here, an approach to evaluate the massive amounts of such data using the resource https://covid19.bioreproducibility.org is described, which offers a template that could be used in large-scale initiatives undertaken in response to future biomedical crises. Broader use of the described methodology could considerably curtail information noise and significantly improve the reproducibility of biomedical research.

findMySequence is presented – a machine-learning method for the identification of unknown proteins and sequence-assignment validation in cryo-EM and X-ray crystallography., Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method’s application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.

We propose BraggNN, a deep-learning based method, to accelerate the most computation-intensive part of polycrystal diffraction data analysis (diffraction signal characterization). The application of BraggNN for real experimental data demonstrates that it can deliver consistent (sometimes even slightly better) results compared with the conventional method while running hundreds of times faster., X-ray diffraction based microscopy techniques such as high-energy diffraction microscopy (HEDM) rely on knowledge of the position of diffraction peaks with high precision. These positions are typically computed by fitting the observed intensities in detector data to a theoretical peak shape such as pseudo-Voigt. As experiments become more complex and detector technologies evolve, the computational cost of such peak-shape fitting becomes the biggest hurdle to the rapid analysis required for real-time feedback in experiments. To this end, we propose BraggNN, a deep-learning based method that can determine peak positions much more rapidly than conventional pseudo-Voigt peak fitting. When applied to a test dataset, peak center-of-mass positions obtained from BraggNN deviate less than 0.29 and 0.57 pixels for 75 and 95% of the peaks, respectively, from positions obtained using conventional pseudo-Voigt fitting (Euclidean distance). When applied to a real experimental dataset and using grain positions from near-field HEDM reconstruction as ground-truth, grain positions using BraggNN result in 15% smaller errors compared with those calculated using pseudo-Voigt. Recent advances in deep-learning method implementations and special-purpose model inference accelerators allow BraggNN to deliver enormous performance improvements relative to the conventional method, running, for example, more than 200 times faster on a consumer-class GPU card with out-of-the-box software.

Experimental and theoretical charge density investigations performed for langbeinite allow for detailed examination of the redistribution of electron density under pressure both within atomic basins as well as at atomic positions., Pressure is well known to dramatically alter physical properties and chemical behaviour of materials, much of which is due to the changes in chemical bonding that accompany compression. Though it is relatively easy to comprehend this correlation in the discontinuous compression regime, where phase transformations take place, understanding of the more subtle continuous compression effects is a far greater challenge, requiring insight into the finest details of electron density redistribution. In this study, a detailed examination of quantitative electron density redistribution in the mineral langbeinite was conducted at high pressure. Langbeinite is a potassium magnesium sulfate mineral with the chemical formula [K2Mg2(SO4)3], and crystallizes in the isometric tetartoidal (cubic) system. The mineral is an ore of potassium, occurs in marine evaporite deposits in association with carnallite, halite and sylvite, and gives its name to the langbeinites, a family of substances with the same cubic structure, a tetrahedral anion, and large and small cations. Single-crystal X-ray diffraction data for langbeinite have been collected at ambient pressure and at 1 GPa using a combination of in-house and synchrotron techniques. Experiments were complemented by theoretical calculations within the pressure range up to 40 GPa. On the basis of changes in structural and thermal parameters, all ions in the langbeinite structure can be grouped into ‘soft’ (potassium cations and oxygens) and ‘hard’ (sulfur and magnesium). This analysis emphasizes the importance of atomic basins as a convenient tool to analyse the redistribution of electron density under external stimuli such as pressure or temperature. Gradual reduction of completeness of experimental data accompanying compression did not significantly reduce the quality of structural, electronic and thermal parameters obtained in experimental quantitative charge density analysis.

High-pressure single-crystal X-ray and neutron diffraction data for copper(II) sulfate pentahydrate have been collected under precisely the same conditions, using the same sample mounted in a miniature diamond-anvil cell. The data were combined in a joint ‘XN’ structure refinement., Single-crystal X-ray and neutron diffraction data are usually collected using separate samples. This is a disadvantage when the sample is studied at high pressure because it is very difficult to achieve exactly the same pressure in two separate experiments, especially if the neutron data are collected using Laue methods where precise absolute values of the unit-cell dimensions cannot be measured to check how close the pressures are. In this study, diffraction data have been collected under the same conditions on the same sample of copper(II) sulfate pentahydrate, using a conventional laboratory diffractometer and source for the X-ray measurements and the Koala single-crystal Laue diffractometer at the ANSTO facility for the neutron measurements. The sample, of dimensions 0.40 × 0.22 × 0.20 mm3 and held at a pressure of 0.71 GPa, was contained in a miniature Merrill–Bassett diamond-anvil cell. The highly penetrating diffracted neutron beams passing through the metal body of the miniature cell as well as through the diamonds yielded data suitable for structure refinement, and compensated for the low completeness of the X-ray measurements, which was only 24% on account of the triclinic symmetry of the sample and the shading of reciprocal space by the cell. The two data-sets were combined in a single ‘XN’ structure refinement in which all atoms, including H atoms, were refined with anisotropic displacement parameters. The precision of the structural parameters was improved by a factor of up to 50% in the XN refinement compared with refinements using the X-ray or neutron data separately.

The syntheses of regioisomers of calix[6]crown-6 under a metal carbonate template were highly metal cation-dependent and the 1,2-bridged isomer (H4 L 1,2) catches Cs+ very efficiently in its deep and good-fit pocket similar to a baseball glove., We report the formation of heavy alkali metal complexes of bicyclic host molecules including the caesium(I) complex that catches the central metal ion with the deep pocket of the host similar to a baseball glove. For this, three regioisomers of singly bridged calix[6]crown-6 [1,2-bridged (H4 L 1,2), 1,3-bridged (H4 L 1,3) and 1,4-bridged (H4 L 1,4)] have been synthesized by alkyl­ation of calix[6]arene with penta­ethyl­ene glycol di­tosyl­ate in the presence of M 2CO3 (M = Na, K, Rb and Cs). The larger the cation size of the metal carbonate, the higher the yield of the H4 L 1,4 isomer, indicating the size-based template effect. A combination of H4 L 1,2 and RbOH allowed isolation of the mononuclear rubidium(I) complex (1) in which the metal center is six-coordinated in a loose fashion, the remaining two oxygen donors in the crown loop and two phenols in the calix rim are uncoordinated. Notably, the complexation of H4 L 1,2 with CsOH yielded the mononuclear caesium(I) complex (2), in which all possible ten binding sites on the deep and good-fit pocket participate in coordination via high cooperativity between the crown loop and calix rim, similar to a baseball glove. In dipolar organic solution, the caesium(I) complex 2 remains intact. H4 L 1,4 afforded a dicesium(I) complex (3) and adjacent complexes are linked by intermolecular cation–π interactions, giving rise to a pseudo one-dimensional coordination polymer. These results provide insight into the metal carbonate-dependent synthesis of calix[6]crowns and the influence of regioisomers on caesium(I) complexation.

IUCrJ 8(6), 905 - 920 (2021). doi:10.1107/S2052252521008046, Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables essentially radiation-damage-free macromolecular structure determination using microcrystals that are too small for synchrotron studies. However, SFX experiments often require large amounts of sample in order to collect highly redundant data where some of the many stochastic errors can be averaged out to determine accurate structure-factor amplitudes. In this work, the capability of the Swiss X-ray free-electron laser (SwissFEL) was used to generate large-bandwidth X-ray pulses [$����/��$ = 2.2% full width at half-maximum (FWHM)], which were applied in SFX with the aim of improving the partiality of Bragg spots and thus decreasing sample consumption while maintaining the data quality. Sensitive data-quality indicators such as anomalous signal from native thaumatin micro-crystals and de novo phasing results were used to quantify the benefits of using pink X-ray pulses to obtain accurate structure-factor amplitudes. Compared with data measured using the same setup but using X-ray pulses with typical quasi-monochromatic XFEL bandwidth (����/�� = 0.17% FWHM), up to fourfold reduction in the number of indexed diffraction patterns required to obtain similar data quality was achieved. This novel approach, pink-beam SFX, facilitates the yet underutilized de novo structure determination of challenging proteins at XFELs, thereby opening the door to more scientific breakthroughs., Published by Chester

Understanding the catalytic mechanism of SARS-CoV-2 main protease (Mpro) can help in guiding drug design of specific small-molecule antivirals. A 2.0 Å resolution room-temperature X-ray crystal structure of inactive C145A mutant Mpro in complex with the octapeptide Ac-SAVLQSGF-CONH2 that resembles a Michaelis complex is reported., SARS-CoV-2 emerged at the end of 2019 to cause an unprecedented pandemic of the deadly respiratory disease COVID-19 that continues to date. The viral main protease (Mpro) is essential for SARS-CoV-2 replication and is therefore an important drug target. Understanding the catalytic mechanism of Mpro, a cysteine protease with a catalytic site comprising the noncanonical Cys145–His41 dyad, can help in guiding drug design. Here, a 2.0 Å resolution room-temperature X-ray crystal structure is reported of a Michaelis-like complex of Mpro harboring a single inactivating mutation C145A bound to the octapeptide Ac-SAVLQSGF-CONH2 corresponding to the nsp4/nsp5 autocleavage site. The peptide substrate is unambiguously defined in subsites S5 to S3′ by strong electron density. Superposition of the Michaelis-like complex with the neutron structure of substrate-free Mpro demonstrates that the catalytic site is inherently pre-organized for catalysis prior to substrate binding. Induced fit to the substrate is driven by P1 Gln binding in the predetermined subsite S1 and rearrangement of subsite S2 to accommodate P2 Leu. The Michaelis-like complex structure is ideal for in silico modeling of the SARS-CoV-2 Mpro catalytic mechanism.

With a view to establishing molecular recognition rules, the host p-tert-butyl­calix[6]arene was crystallized with different guest molecules. The ratio between the apolar surface area and the volume was used to predict the formation of inclusion versus exclusion complexes, with inclusion complexes observed at ratios, Calixarenes are host molecules that can form complexes with one or more guest molecules, and molecular recognition in calixarenes can be affected by many factors. With a view to establishing molecular recognition rules, the host p-tert-butyl­calix[6]arene (TBC6) was crystallized with different guest molecules (cyclo­hexane, anisole, heptane, toluene, benzene, methyl acetate, ethyl acetate, di­chloro­methane, tetra­hydro­furan and pyridine) and the obtained structures were characterized by X-ray diffraction. With most solvents, 1:1 and/or 1:3 host–guest complexes were formed, although other stoichiometries were also observed with small guest molecules, and crystallization from ethyl acetate produced the unsolvated form. The calculated fill percentage of the TBC6 cavity was ∼55% for apolar guests and significantly lower for polar solvents, indicating that polar molecules can bind to apolar cavities with significantly lower packing coefficients. The most stable crystals were formed by 1:1 host–guest inclusion complexes. The ratio between the apolar surface area and the volume was used to predict the formation of inclusion versus exclusion complexes, with inclusion complexes observed at ratios

For the first time, AA h boron nitride (BN) crystal, assigned to an orthorhombic space group (No. 31, Pm21), is reported. The structure of BN nanotubes is reinterpreted as a helix, resulting from texture and helical growth of the AA h BN crystal used., AA h boron nitride (BN) crystal, assigned to an orthorhombic space group (No. 31, Pm21), is reported here. This new AA h BN crystal exhibits a ‘linear’ morphology for high-resolution transmission electron microscopy (HRTEM) and a (non-hexagonal) ‘diagonal’ electron-diffraction pattern, which have been experimentally demonstrated in this article. It is also demonstrated that this new crystal is the basic structure of multi-walled BN nanotubes (BNNTs) existing in the form of a helix. The helical AA h BNNTs exist in a metastable phase owing to 〈200〉 texture growth of the orthorhombic crystal, where the energy is ∼15 meV higher than that of stable AB or AA′ BN. It is shown that the typical scanning electron microscope ‘fluffy cotton-like’ morphology of BNNTs is due to secondary growth of diverse BN sheets (including mono-layers) on incoherently scrolled wall strands of BNNTs, providing further evidence for the helical structure with HRTEM evidence for a left-handed helix.

The influence of a diamond anvil cell (DAC) aperture, incident radiation wavelength and sample orientation in a DAC on the completeness of diffraction data collected at high pressure has been systematically analyzed. The considerable impact of sample orientation on achievable data completeness has been confirmed and quantified for all Laue classes in the form of graphical guides. These guides have been applied to predict sample orientation for structural analysis of a sample undergoing an orthorhombic → monoclinic phase transition under pressure which ensured over 90% completeness., Sufficiently high completeness of diffraction data is necessary to correctly determine the space group, observe solid-state structural transformations or investigate charge density distribution under pressure. Regrettably, experiments performed at high pressure in a diamond anvil cell (DAC) yield inherently incomplete datasets. The present work systematizes the combined influence of radiation wavelength, DAC opening angle and sample orientation in a DAC on the completeness of diffraction data collected in a single-crystal high-pressure (HP) experiment with the help of dedicated software. In particular, the impact of the sample orientation on the achievable data completeness is quantified and proved to be substantial. Graphical guides for estimating the most beneficial sample orientation depending on the sample Laue class and assuming a few commonly used experimental setups are proposed. The usefulness of these guides has been tested in the case of luminescent 1,3-diacetylpyrene, suspected to undergo transitions from the α phase (Pnma) to the γ phase (Pn21 a) and δ phase (P1121/a) under pressure. Effective sample orientation has ensured over 90% coverage even for the monoclinic system and enabled unrestrained structure refinements and access to complete systematic extinction patterns.

A new tool based on 3D Zernike polynomials is presented that allows the study of the continuous heterogeneity of biological macromolecules, revealing the structural relationships present among different states by the approximation of deformation fields., Structural biology has evolved greatly due to the advances introduced in fields like electron microscopy. This image-capturing technique, combined with improved algorithms and current data processing software, allows the recovery of different conformational states of a macromolecule, opening new possibilities for the study of its flexibility and dynamic events. However, the ensemble analysis of these different conformations, and in particular their placement into a common variable space in which the differences and similarities can be easily recognized, is not an easy matter. To simplify the analysis of continuous heterogeneity data, this work proposes a new automatic algorithm that relies on a mathematical basis defined over the sphere to estimate the deformation fields describing conformational transitions among different structures. Thanks to the approximation of these deformation fields, it is possible to describe the forces acting on the molecules due to the presence of different motions. It is also possible to represent and compare several structures in a low-dimensional mapping, which summarizes the structural characteristics of different states. All these analyses are integrated into a common framework, providing the user with the ability to combine them seamlessly. In addition, this new approach is a significant step forward compared with principal component analysis and normal mode analysis of cryo-electron microscopy maps, avoiding the need to select components or modes and producing localized analysis.

Crystal structures of oxy–deoxy intermediates of a 400 kDa giant hemoglobin reveal the allosteric transition intermediates of the unmodified protein and unrestrained oxygen saturation, which have been missing pieces in the study of the allosteric behavior of hemoglobins over the last half century., Cooperative oxygen binding of hemoglobin (Hb) has been studied for over half a century as a representative example of the allostericity of proteins. The most important problem remaining to be solved is the lack of structural information on the intermediates between the oxygenated and deoxygenated forms. In order to characterize the intermediate structures, it is necessary to obtain intermediate-state crystals, determine their oxygen saturations and then determine the oxygen saturations of each of their constituent subunits, all of which are challenging issues even now. Here, intermediate forms of the 400 kDa giant Hb from the tubeworm Oligobrachia mashikoi are reported. To overcome the above problems without any artificial modifications to the protein or prosthetic groups, intermediate crystals of the giant Hb were prepared from fully oxygenated crystals by a soaking method. The oxygen saturation of the crystals was measured by in situ observation with a microspectrophotometer using thin plate crystals processed by an ultraviolet laser to avoid saturation of absorption. The oxygen saturation of each subunit was determined by occupancy refinement of the bound oxygen based on ambient temperature factors. The obtained structures reveal the detailed relationship between the structural transition and oxygen dissociation. The dimer subassembly of the giant Hb shows strong correlation with the local structural changes at the heme pockets. Although some local ternary-structural changes occur in the early stages of the structural transition, the associated global ternary-structural and quaternary-structural changes might arise at about 50% oxygen saturation. The models based on coarse snapshots of the allosteric transition support the conventional two-state model of Hbs and provide the missing pieces of the intermediate structures that are required for full understanding of the allosteric nature of Hbs in detail.

Higher X-ray energies are experimentally demonstrated to be highly beneficial for macromolecular crystallography., X-ray-induced radiation damage is a limiting factor for the macromolecular crystallographer and data must often be merged from many crystals to yield complete data sets for the structure solution of challenging samples. Increasing the X-ray energy beyond the typical 10–15 keV range promises to provide an extension of crystal lifetime via an increase in diffraction efficiency. To date, however, hardware limitations have negated any possible gains. Through the first use of a cadmium telluride EIGER2 detector and a beamline optimized for high-energy data collection, it is shown that at higher energies fewer crystals will be required to obtain complete data, as the diffracted intensity per unit dose increases by a factor of more than two between 12.4 and 25 keV. Additionally, these higher energy data can provide more information, as shown by a systematic increase in the high-resolution cutoff of the data collected. Taken together, these gains point to a high-energy future for synchrotron-based macromolecular crystallography.

A method of regulating the crystallization of conformational polymorphs based on the crystal structure similarity of templates and the target crystal form has been developed., Template design on polymorph control, especially conformational polymorphs, is still in its infancy and the result of polymorph control is often accidental. A method of regulating the crystallization of conformational polymorphs based on the crystal structure similarity of templates and the target crystal form has been developed. Crystal structure similarity was considered to be able to introduce lattice matching (geometric term) with chemical interactions to regulate conformational polymorph nucleation. The method was successfully applied to induce the crystallization of DA7-II [HOOC–(CH2)n −2–COOH (diacids), named DAn, where n = 7, 9, 15, 17 and II represents the metastable polymorph] on the surface of DA15-II. An analogous two-dimensional plane – the (002) face of both DA15-II and DA7-II – was firstly predicted as the epitaxially attached face with similar lattice parameters and the strongest adsorption energy. The powder DA15-II template with the preferred orientation face in (002) presented much stronger inducing DA7-II ability than the template with other preferred orientation faces. The epitaxial growth of DA7-II on DA15-II through an identical (002) face was clearly observed and verified by the single-crystal inducing experiments. The molecular dynamics simulation results demonstrated that the strong interactions occurred between DA7 molecules and the (002) face of DA15-II. This method has been verified and further applied to the crystallization of DA7-II on the surface of DA17-II and DA9-II on the surface of DA15-II. This study developed a strategy based on structure similarity to regulate the conformational polymorph and verified the significant role of lattice matching and chemical effects on the design and preparation of templates.

The UnitCell Tools package was developed to determine unit-cell parameters of a crystal from a single electron diffraction pattern with high-order Laue zone reflections acquired in the conventional transmission electron microscope., Electron diffraction techniques in transmission electron microscopy (TEM) have been successfully employed for determining the unit-cell parameters of crystal phases, albeit they exhibit a limited accuracy compared with X-ray or neutron diffraction, and they often involve a tedious measurement procedure. Here, a new package for determining unit-cell parameters from a single electron diffraction pattern has been developed. The essence of the package is to reconstruct a 3D reciprocal primitive cell from a single electron diffraction pattern containing both zero-order Laue zone and high-order Laue zone reflections. Subsequently, the primitive cell can be reduced to the Niggli cell which, in turn, can be converted into the unit cell. Using both simulated and experimental patterns, we detail the working procedure and address some effects of experimental conditions (diffraction distortions, misorientation of the zone axis and the use of high-index zone axis) on the robustness and accuracy of the software developed. The feasibility of unit-cell determination of the TiO2 nanorod using this package is also demonstrated. Should the parallel-beam, nano-beam and convergent-beam modes of the TEM be used flexibly, the software can determine unit-cell parameters of unknown-structure crystallites (typically >50 nm).

Improvements in cryo-trapping technology enable single-crystal time-resolved crystallography of an enzyme with 40 ms time resolution., Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and the complex experimental infrastructure that are required remain serious obstacles to its widespread application. Here, millisecond mix-and-quench crystallography (MMQX) has been developed, which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxy­kinase (PEPCK) is observed with a time resolution of 40 ms. By lowering the entry barrier to time-resolved crystallography, MMQX should enable a broad expansion in structural studies of protein dynamics.

This paper presents a detailed assessment of the performance of the CRYO ARM 300 electron microscope in a multiuser cryo-EM facility setting. It is shown that the microscope can be used for reliable automated data collection. The strengths and weaknesses of the hardware are discussed., Single-particle cryo-EM has become an indispensable structural biology method. It requires regular access to high-resolution electron cryogenic microscopes. To fully utilize the capacity of the expensive high-resolution instruments, the time used for data acquisition and the rate of data collection have to be maximized. This in turn requires high stability and high uptime of the instrument. One of the first 300 kV JEOL CRYO ARM 300 microscopes has been installed at the cryo-EM facility BECM at VIB-VUB, Brussels, where the microscope is used for continuous data collection on multiple projects. Here, the suitability and performance of the microscope is assessed for high-throughput single-particle data collection. In particular, the properties of the illumination system, the stage stability and ice contamination rates are reported. The microscope was benchmarked using mouse heavy-chain apoferritin which was reconstructed to a resolution of 1.9 Å. Finally, uptime and throughput statistics of the instrument accumulated during the first six months of the facility operation in user access mode are reported.

A new geometrical approach is proposed for finding the most prominent planar gaps/cleavage planes in crystal structures. The approach is realized by using the GALOCS program package and is demonstrated on several inorganic structures., Cleavage is the ability of single crystals to split easily along specifically oriented planes. This phenomenon is of great interest for materials’ scientists. Acquiring the data regarding cleavage is essential for the understanding of brittle fracture, plasticity and strength, as well as for the prevention of catastrophic device failures. Unfortunately, theoretical calculations of cleavage energy are demanding and often unsuitable for high-throughput searches of cleavage planes in arbitrary crystal structures. A simplified geometrical approach (GALOCS = gaps locations in crystal structures) is suggested for predicting the most promising cleavage planes. GALOCS enumerates all the possible reticular lattice planes and calculates the plane-average electron density as a function of the position of the planes in the unit cell. The assessment of the cleavage ability of the planes is based on the width and depth of planar gaps in crystal structures, which appear when observing the planes lengthwise. The method is demonstrated on two-dimensional graphene and three-dimensional silicon, quartz and LiNbO3 structures. A summary of planar gaps in a few more inorganic crystal structures is also presented.

Small-angle X-ray scattering and tryptophan fluorescence studies of phospho­ethano­lamine transferase (EptA) suggest conformational flexibility linked to enzyme activity., Many pathogenic gram-negative bacteria have developed mechanisms to increase resistance to cationic antimicrobial peptides by modifying the lipid A moiety. One modification is the addition of phospho­ethano­lamine to lipid A by the enzyme phospho­ethano­lamine transferase (EptA). Previously we reported the structure of EptA from Neisseria, revealing a two-domain architecture consisting of a periplasmic facing soluble domain and a transmembrane domain, linked together by a bridging helix. Here, the conformational flexibility of EptA in different detergent environments is probed by solution scattering and intrinsic fluorescence-quenching studies. The solution scattering studies reveal the enzyme in a more compact state with the two domains positioned close together in an n-do­decyl-β-d-maltoside micelle environment and an open extended structure in an n-do­decyl-phospho­choline micelle environment. Intrinsic fluorescence quenching studies localize the domain movements to the bridging helix. These results provide important insights into substrate binding and the molecular mechanism of endotoxin modification by EptA.

C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. Two X-ray crystallographic studies are presented of the antibody RoAb13, which binds to the peptide PIYDIN, which is part of the N-terminal domain of CCR5. The results may provide the basis for active immunization vaccines to stimulate an antibody response to native CCR5 that will block HIV infection., C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. This led to the hypothesis that stimulating an antibody response would block HIV with minimal toxicity. Here, X-ray crystallographic studies of the anti-CCR5 antibody RoAb13 together with two peptides were undertaken: one peptide is a 31-residue peptide containing the PIYDIN sequence and the other is the PIDYIN peptide alone, where PIYDIN is part of the N-terminal region of CCR5 previously shown to be important for HIV entry. In the presence of the longer peptide (the complete N-terminal domain), difference electron density was observed at a site within a hypervariable CDR3 binding region. In the presence of the shorter core peptide PIYDIN, difference electron density is again observed at this CDR3 site, confirming consistent binding for both peptides. This may be useful in the design of a new biomimetic to stimulate an antibody response to CCR5 in order to block HIV infection.

The present laboratory diffraction contrast tomography suffers from poor spatial resolution – only grains larger than 40 µm can be reliably imaged. In this work, it is shown how this serious limitation can be lifted and the spatial resolution improved significantly., Laboratory diffraction contrast tomography (LabDCT) is a novel technique for non-destructive imaging of the grain structure within polycrystalline samples. To further broaden the use of this technique to a wider range of materials, both the spatial resolution and detection limit achieved in the commonly used Laue focusing geometry have to be improved. In this work, the possibility of improving both grain indexing and shape reconstruction was investigated by increasing the sample-to-detector distance to facilitate geometrical magnification of diffraction spots in the LabDCT projections. LabDCT grain reconstructions of a fully recrystallized iron sample, obtained in the conventional Laue focusing geometry and in a magnified geometry, are compared to one characterized by synchrotron X-ray diffraction contrast tomography, with the latter serving as the ground truth. It is shown that grain indexing can be significantly improved in the magnified geometry. It is also found that the magnified geometry improves the spatial resolution and the accuracy of the reconstructed grain shapes. The improvement is shown to be more evident for grains smaller than 40 µm than for larger grains. The underlying reasons are clarified by comparing spot features for different LabDCT datasets using a forward simulation tool.

Ubiquitous defects in polycrystalline powders and single crystals affect the pathways of polymorphic solid-to-solid phase transitions. Dependent on the density of crystal defects, the phase transition mechanism can be dominated by either the cooperative molecular motion pathway or the nucleation and growth pathway., Understanding of solid-to-solid phase transition mechanisms in polymorphic systems is of critical importance for rigorous control over polymorph purity in the pharmaceutical industry to achieve the desired bioavailability and efficacy of drugs. Ubiquitous defects in crystals may play an important role in the pathways of phase transitions. However, such effects remain poorly understood. Here, the effects of crystal defects on the solid-to-solid phase transformations between dl-me­thio­nine polymorphs α and β are investigated by means of experimental and computational approaches. Thermal analyses of polycrystalline powders show two endothermic peaks in the α-to-β phase transition (and two exothermic peaks for the reverse transition), in contrast with one thermal event observed for single crystals. Variable-temperature 1D and 2D Raman spectra, as well as powder X-ray diffraction patterns, reveal the appearance of two peaks that can attributed to a two-step phase transition, and the extent of the second-step phase transition increases with milling time (or defect density). Quantification of transition kinetics unveils a remarkably higher energy barrier in the second-step phase transition than in the first, proceeding by the cooperative molecular motion pathway. The good linear fitting on the kinetic data by the Jeziorny model suggests that the second-step transition follows the nucleation and growth mechanism. Molecular dynamics simulations were also conducted to understand the role of crystal defects in the solid-state phase transition by tracking the atomic distribution and hydrogen bond lifetime during the transition. It was found that the increasing defect density hinders the propagation of cooperative molecular motion, leading to a combined transition mechanism involving both cooperative motion and nucleation and growth. This study highlights the significant impact of crystal defects on solid-state phase transitions, and the two-step transition mechanism postulated may be universal given the ubiquitous presence of defects in crystalline materials.

A deep learning neural network has been developed to efficiently and accurately clean the background noise in experimental lab-based X-ray diffraction images. A better spot segmentation is obtained and thus grain mapping in 3D is improved compared with the conventional method., Laboratory X-ray diffraction contrast tomography (LabDCT) is a novel imaging technique for non-destructive 3D characterization of grain structures. An accurate grain reconstruction critically relies on precise segmentation of diffraction spots in the LabDCT images. The conventional method utilizing various filters generally satisfies segmentation of sharp spots in the images, thereby serving as a standard routine, but it also very often leads to over or under segmentation of spots, especially those with low signal-to-noise ratios and/or small sizes. The standard routine also requires a fine tuning of the filtering parameters. To overcome these challenges, a deep learning neural network is presented to efficiently and accurately clean the background noise, thereby easing the spot segmentation. The deep learning network is first trained with input images, synthesized using a forward simulation model for LabDCT in combination with a generic approach to extract features of experimental backgrounds. Then, the network is applied to remove the background noise from experimental images measured under different geometrical conditions for different samples. Comparisons of both processed images and grain reconstructions show that the deep learning method outperforms the standard routine, demonstrating significantly better grain mapping.

The glycosyltransferase MurG from the human pathogen A. baumannii was characterized and its hexameric crystal structure was unveiled. This is the first homo-oligomeric structure to be described in the MurG family and the Mur family. The homo-oligomerization mechanism of MurG is clarified, thus opening the door for the design of next-generation antibiotics that target MurG., Lipid II, the main component of the bacterial cell wall, is synthesized by the addition of UDP-N-acetylglucosamine to the UDP-N-acetylmuramic acid pentapeptide catalyzed by the glycosyltransferase MurG. Owing to its critical role in cell-wall biosynthesis, MurG is considered to be an attractive target for antibacterial agents. Although the Mur family ligases have been extensively studied, the molecular mechanism of the oligomeric scaffolding assembly of MurG remains unclear. In this study, MurG from Acinetobacter baumannii (abMurG), a human pathogen, was characterized and its hexameric crystal structure was unveiled; this is the first homo-oligomeric structure to be described in the MurG family and the Mur family. Homogeneous protein samples were produced for structural studies using size-exclusion chromatography, the absolute molecular mass was calculated via multi-angle light scattering, and protein–protein interactions were analyzed using the PDBePISA server. abMurG was found to form homo-oligomeric complexes in solution, which might serve as functional units for the scaffolding activity of MurG. Furthermore, analysis of this structure revealed the molecular assembly mechanism of MurG. This structural and biochemical study elucidated the homo-oligomerization mechanism of MurG and suggests a new potential antibiotic target on MurG.

IUCrJ 8(4), 665 - 677 (2021). doi:10.1107/S2052252521005297, The crystallization of recombinant proteins in living cells is an exciting new approach in structural biology. Recent success has highlighted the need for fast and efficient diffraction data collection, optimally directly exposing intact crystal-containing cells to the X-ray beam, thus protecting the in cellulo crystals from environmental challenges. Serial femtosecond crystallography (SFX) at free-electron lasers (XFELs) allows the collection of detectable diffraction even from tiny protein crystals, but requires very fast sample exchange to utilize each XFEL pulse. Here, an efficient approach is presented for high-resolution structure elucidation using serial femtosecond in cellulo diffraction of micometre-sized crystals of the protein HEX-1 from the fungus Neurospora crassa on a fixed target. Employing the fast and highly accurate Roadrunner II translation-stage system allowed efficient raster scanning of the pores of micro-patterned, single-crystalline silicon chips loaded with living, crystal-containing insect cells. Compared with liquid-jet and LCP injection systems, the increased hit rates of up to 30% and reduced background scattering enabled elucidation of the HEX-1 structure. Using diffraction data from only a single chip collected within 12 min at the Linac Coherent Light Source, a 1.8 Å resolution structure was obtained with significantly reduced sample consumption compared with previous SFX experiments using liquid-jet injection. This HEX-1 structure is almost superimposable with that previously determined using synchrotron radiation from single HEX-1 crystals grown by sitting-drop vapour diffusion, validating the approach. This study demonstrates that fixed-target SFX using micro-patterned silicon chips is ideally suited for efficient in cellulo diffraction data collection using living, crystal-containing cells, and offers huge potential for the straightforward structure elucidation of proteins that form intracellular crystals at both XFELs and synchrotron sources., Published by Chester

X-ray diffraction tensor tomography is used to map clay mineral orientation and high-density inclusions in a sample of Pierre shale., Shales have a complex mineralogy with structural features spanning several length scales, making them notoriously difficult to fully understand. Conventional attenuation-based X-ray computed tomography (CT) measures density differences, which, owing to the heterogeneity and sub-resolution features in shales, makes reliable interpretation of shale images a challenging task. CT based on X-ray diffraction (XRD-CT), rather than intensity attenuation, is becoming a well established technique for non-destructive 3D imaging, and is especially suited for heterogeneous and hierarchical materials. XRD patterns contain information about the mineral crystal structure, and crucially also crystallite orientation. Here, we report on the use of orientational imaging using XRD-CT to study crystallite-orientation distributions in a sample of Pierre shale. Diffraction-contrast CT data for a shale sample measured with its bedding-plane normal aligned parallel to a single tomographic axis perpendicular to the incoming X-ray beam are discussed, and the spatial density and orientation distribution of clay minerals in the sample are described. Finally, the scattering properties of highly attenuating inclusions in the shale bulk are studied, which are identified to contain pyrite and clinochlore. A path forward is then outlined for systematically improving the structural description of shales.

The mechanism of a solid–solid phase transition in an RNA crystal is presented., Solid–solid phase transitions (SSPTs) occur between distinguishable crystalline forms. Because of their importance in application and theory in materials science and condensed-matter physics, SSPTs have been studied most extensively in metallic alloys, inorganic salts and small organic molecular crystals, but much less so in biomacromolecular crystals. In general, the mechanisms of SSPTs at the atomic and molecular levels are not well understood. Here, the ordered molecular rearrangements in biomacromolecular crystals of the adenine riboswitch aptamer are described using real-time serial crystallography and solution atomic force microscopy. Large, ligand-induced conformational changes drive the initial phase transition from the apo unit cell (AUC) to the trans unit cell 1 (TUC1). During this transition, coaxial stacking of P1 duplexes becomes the dominant packing interface, whereas P2–P2 interactions are almost completely disrupted, resulting in ‘floating’ layers of molecules. The coupling points in TUC1 and their local conformational flexibility allow the molecules to reorganize to achieve the more densely packed and energetically favorable bound unit cell (BUC). This study thus reveals the interplay between the conformational changes and the crystal phases – the underlying mechanism that drives the phase transition. Using polarized video microscopy to monitor SSPTs in small crystals at high ligand concentration, the time window during which the major conformational changes take place was identified, and the in crystallo kinetics have been simulated. Together, these results provide the spatiotemporal information necessary for informing time-resolved crystallography experiments. Moreover, this study illustrates a practical approach to characterization of SSPTs in transparent crystals.

The crystal structure of CYP105D18 and its unique structural features for papaverine N-oxidation are presented., The bacterial CYP105 family is involved in secondary metabolite biosynthetic pathways and plays essential roles in the biotransformation of xenobiotics. This study investigates the newly identified H2O2-mediated CYP105D18 from Streptomyces laurentii as the first bacterial CYP for N-oxidation. The catalytic efficiency of CYP105D18 for papaverine N-oxidation was 1.43 s−1 µM −1. The heme oxidation rate (k) was low (

Distinct ‘hidden’ phases of a technologically relevant thermoelectric material, which are identical in terms of composition and periodic crystal structure, but differ on a local scale, are observed and can be controlled through synthesis conditions. The local structure is explained in terms of a vacancy repulsion model, and relaxations around vacancies are characterized., Although crystalline solids are characterized by their periodic structures, some are only periodic on average and deviate on a local scale. Such disordered crystals with distinct local structures have unique properties arising from both collective and localized behaviour. Different local orderings can exist with identical average structures, making their differences hidden to Bragg diffraction methods. Using high-quality single-crystal X-ray diffuse scattering the local order in thermoelectric half-Heusler Nb1−x CoSb is investigated, for which different local orderings are observed. It is shown that the vacancy distribution follows a vacancy repulsion model and the crystal composition is found always to be close to x = 1/6 irrespective of nominal sample composition. However, the specific synthesis method controls the local order and thereby the thermoelectric properties thus providing a new frontier for tuning material properties.

This work shows the importance of counterintuitive ultra long distances, intramolecular preagostic attractive C—H⋯Ni/Cu and C—H⋯O, C—H⋯H—C contacts and a bunch of other extremely strong non-classic mainly London dispersion driven intermolecular interactions involving C—H bonds: C—H⋯X (X = H—C, N, O, π) in the crystal structures of the NiII and CuII based complexes fabricated from the sterically crowding cyclo­hexyl-containing Schiff base dyes. Photophysical properties of the reported complexes are also discussed., This work reports on synthesis and extensive experimental and theoretical investigations on photophysical, structural and thermal properties of the NiII and CuII discrete mononuclear homoleptic complexes [Ni(L I,II)2] and [Cu(L I,II)2] fabricated from the Schiff base dyes o-HOC6H4—CH=N—cyclo-C6H11 (HL I) and o-HOC10H6—CH=N—cyclo-C6H11 (HL II), containing the sterically crowding cyclo­hexyl units. The six-membered metallocycles adopt a clearly defined envelope conformation in [Ni(L II)2], while they are much more planar in the structures of [Ni(L I)2] and [Cu(L I,II)2]. It has been demonstrated by in-depth bonding analyses based on the ETS-NOCV and Interacting Quantum Atoms energy-decomposition schemes that application of the bulky substituents, containing several C—H groups, has led to the formation of a set of classical and unintuitive intra- and inter-molecular interactions. All together they are responsible for the high stability of [Ni(L I,II)2] and [Cu(L I,II)2]. More specifically, London dispersion dominated intramolecular C—H⋯O, C—H⋯N and C—H⋯H—C hydrogen bonds are recognized and, importantly, the attractive, chiefly the Coulomb driven, preagostic (not repulsive anagostic) C—H⋯Ni/Cu interactions have been discovered despite their relatively long distances (∼2.8–3.1 Å). All the complexes are further stabilized by the extremely efficient intermolecular C—H⋯π(benzene) and C—H⋯π(chelate) interactions, where both the charge-delocalization and London dispersion constituents appear to be crucial for the crystal packing of the obtained complexes. All the complexes were found to be photoluminescent in CH2Cl2, with [Cu(L II)2] exhibiting the most pronounced emission – the time-dependent density-functional-theory computations revealed that it is mostly caused by metal-to-ligand charge-transfer transitions.

The importance of self-association and desolvation in the process of crystal nucleation is emphasized; the rearrangement of supramolecular structures also has a non-negligible effect on the nucleation kinetics., As the first step in the crystallization process, nucleation has been studied by many researchers. In this work, phenacetin (PHEN) was selected as a model compound to investigate the relationship between the solvent and nucleation kinetics. Induction times at different supersaturation in six solvents were measured. FTIR and NMR spectroscopy were employed to explore the solvent–solute interactions and the self-association properties in solution. Density functional theory (DFT) was adopted to evaluate the strength of solute–solvent interactions and the molecular conformations in different solvents. Based on these spectroscopy data, molecular simulation and nucleation kinetic results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics is discussed. Both the solute–solvent interaction strength and the supramolecular structure formed by the self-association of solute molecules affect the nucleation rate. The findings reported here shed new light on the molecular mechanism of nucleation in solution.

Low dislocation density of α-Ga2O3 grown on conical frustum-patterned sapphire substrate (CF-PSS) has been studied. The threading dislocation propagation path of α-Ga2O3 on CF-PSS was observed., The compound α-Ga2O3 is an ultra-wide-bandgap semiconductor and possesses outstanding properties such as a high breakdown voltage and symmetry compared with other phases. It has been studied for applications in high-performance power devices. However, it is difficult to obtain a high-quality thin films because α-Ga2O3 can only grow heteroepitaxially, which results in residual stress generation owing to lattice mismatch and thermal expansion between the substrate and α-Ga2O3. To overcome this, α-Ga2O3 was grown on a conical frustum-patterned sapphire substrate by halide vapor-phase epitaxy. The surface morphology was crack-free and flat. The α-Ga2O3 grown on a frustum-patterned substrate and a conventional sapphire substrate at 500°C exhibited full-width at half-maxima of 961 and 1539 arcsec, respectively, for 10–12 diffraction. For the former substrate, lateral growth on the pattern and threading dislocation bending towards the pattern suppressed the propagation of threading dislocations generated at the interface, which reduced the threading dislocation propagation to the surface by half compared with that on the latter conventional substrate. The results suggest that conical frustum-patterned sapphire substrates have the potential to produce high-quality α-Ga2O3 epilayers.

A framework is described for the efficient and realistic simulation of X-ray diffraction scans to train machine- or deep-learning models like convolutional neural networks for the automatic phase-identification task in multiphase compounds., Within the domain of analyzing powder X-ray diffraction (XRD) scans, manual examination of the recorded data is still the most popular method, but it requires some expertise and is time consuming. The usual workflow for the phase-identification task involves software for searching databases of known compounds and matching lists of d spacings and related intensities to the measured data. Most automated approaches apply some iterative procedure for the search/match process but fail to be generally reliable yet without the manual validation step of an expert. Recent advances in the field of machine and deep learning have led to the development of algorithms for use with diffraction patterns and are producing promising results in some applications. A limitation, however, is that thousands of training samples are required for the model to achieve a reliable performance and not enough measured samples are available. Accordingly, a framework for the efficient generation of thousands of synthetic XRD scans is presented which considers typical effects in realistic measurements and thus simulates realistic patterns for the training of machine- or deep-learning models. The generated data set can be applied to any machine- or deep-learning structure as training data so that the models learn to analyze measured XRD data based on synthetic diffraction patterns. Consequently, we train a convolutional neural network with the simulated diffraction patterns for application with iron ores or cements compounds and prove robustness against varying unit-cell parameters, preferred orientation and crystallite size in synthetic, as well as measured, XRD scans.

A method for determining the sample flow rate and concomitant light condition in time-resolved serial femtosecond crystallography is developed to analyze the intermediate-state structures of photosystem II., Photosystem II (PSII) catalyzes light-induced water oxidation through an Si-state cycle, leading to the generation of di-oxygen, protons and electrons. Pump–probe time-resolved serial femtosecond crystallography (TR-SFX) has been used to capture structural dynamics of light-sensitive proteins. In this approach, it is crucial to avoid light contamination in the samples when analyzing a particular reaction intermediate. Here, a method for determining a condition that avoids light contamination of the PSII microcrystals while minimizing sample consumption in TR-SFX is described. By swapping the pump and probe pulses with a very short delay between them, the structural changes that occur during the S1-to-S2 transition were examined and a boundary of the excitation region was accurately determined. With the sample flow rate and concomitant illumination conditions determined, the S2-state structure of PSII could be analyzed at room temperature, revealing the structural changes that occur during the S1-to-S2 transition at ambient temperature. Though the structure of the manganese cluster was similar to previous studies, the behaviors of the water molecules in the two channels (O1 and O4 channels) were found to be different. By comparing with the previous studies performed at low temperature or with a different delay time, the possible channels for water inlet and structural changes important for the water-splitting reaction were revealed.

The experimental electron-density distribution in a titanium peroxo complex has been studied and compared with theoretical results., An extensive characterization of [Ti(C22H18N2O6)]·H2O was performed by topological analysis according to Bader’s quantum theory of atoms in molecules (QTAIM) from the experimentally (multipole model) and theoretically (DFT) determined electron density. To the best of our knowledge, this study is the first example of an experimental electronic structure of a coordination compound in which a peroxo anion is bonded to a 3d central atom. The titanium coordination polyhedron could be described as a deformed tetrahedral pyramid if the midpoint of the peroxide O—O bond (side-on mode) is considered to be in the quasi-apical position. According to the multipole model (MM) results, the titanium atom has a positive QTAIM charge of 2.05 e− which does not correspond to the formal Ti (IV) oxidation state. On the other hand, the peroxo oxygen atoms O(1) and O(2) have MM QTAIM charges of −0.27 and −0.12, respectively. This asymmetric charge density distribution on the peroxo oxygens is in agreement with the distorted orientation of the O2 moiety with respect to the titanium atom. Despite the fact that the overall MM charge of the O2 moiety is more remote from the formal −2 charge than from neutral O2, the O—O distance remains close to that in the peroxo O2 2− anion. In the case of DFT results, the titanium atom charge is also found to be close to +2, the O2 x− moiety charge is around −1, the optimized O—O distance is shorter by only ca 0.04 Å than the experimental value of 1.5005 (16) Å, and the DFT d-populations on titanium are found to be lower than the experimental MM value. This study is the first experimental electronic structure of a transition metal peroxo complex.

IUCrJ 8(2), 208 - 214 (2021). doi:10.1107/S2052252521000075, At high pressures, autoionization – along with polymerization and metallization – is one of the responses of simple molecular systems to a rise in electron density. Nitro­sonium nitrate (NO$^+$NO$_3$$^{−}$), known for this property, has attracted a large interest in recent decades and was reported to be synthesized at high pressure and high temperature from a variety of nitro­gen–oxygen precursors, such as N$_2$O$_4$, N$_2$O and N$_2$–O$_2$ mixtures. However, its structure has not been determined unambiguously. Here, we present the first structure solution and refinement for nitro­sonium nitrate on the basis of single-crystal X-ray diffraction at 7.0 and 37.0 GPa. The structure model (P2$_1$/m space group) contains the triple-bonded NO$^+$ cation and the NO$_{3}$$^{−}$ sp$^2$-trigonal planar anion. Remarkably, crystal-chemical considerations and accompanying density-functional-theory calculations show that the oxygen atom of the NO$^+$ unit is positively charged – a rare occurrence when in the presence of a less-electronegative element., Published by Chester

The whole pair distribution function modeling method is introduced to overcome the distinction between Bragg and Debye theories in analysis of powder-scattering data. Models based on Bragg’s law are used to facilitate the computation of a whole pair distribution function followed by the solution of the Debye scattering equation., Microstructure-based design of materials requires an atomic level understanding of the mechanisms underlying structure-dependent properties. Methods for analyzing either the traditional diffraction profile or the pair distribution function (PDF) differ in how the information is accessed and in the approximations usually applied. Any variation of structural and microstructural features over the whole sample affects the Bragg peaks as well as any diffuse scattering. Accuracy of characterization relies, therefore, on the reliability of the analysis methods. Methods based on Bragg’s law investigate the diffraction peaks in the intensity plot as distinct pieces of information. This approach reaches a limitation when dealing with disorder scenarios that do not conform to such a peak-by-peak basis. Methods based on the Debye scattering equation (DSE) are, otherwise, well suited to evaluate the scattering from a disordered phase but the structure information is averaged over short-range distances usually accessed by experiments. Moreover, statistical reliability is usually sacrificed to recover some of the computing-efficiency loss compared with traditional line-profile-analysis methods. Here, models based on Bragg’s law are used to facilitate the computation of a whole PDF and then model powder-scattering data via the DSE. Models based on Bragg’s law allow the efficient solution of the dispersion of a crystal’s properties in a powder sample with statistical reliability, and the PDF provides the flexibility of the DSE. The whole PDF is decomposed into the independent directional components, and the number of atom pairs separated by a given distance is statistically estimated using the common-volume functions. This approach overcomes the need for an atomistic model of the material sample and the computation of billions of pair distances. The results of this combined method are in agreement with the explicit solution of the DSE although the computing efficiency is comparable with that of methods based on Bragg’s law. Most importantly, the method exploits the strengths and different sensitivities of the Bragg and Debye theories.

Over 100 models of SARS-CoV-2 3CLpro, a major drug-design target for COVID-19, have been carefully validated and assembled in a dedicated database. Their comparative analysis provides lessons for similar medically oriented efforts and for structural biology in general., The appearance at the end of 2019 of the new SARS-CoV-2 coronavirus led to an unprecedented response by the structural biology community, resulting in the rapid determination of many hundreds of structures of proteins encoded by the virus. As part of an effort to analyze and, if necessary, remediate these structures as deposited in the Protein Data Bank (PDB), this work presents a detailed analysis of 81 crystal structures of the main protease 3CLpro, an important target for the design of drugs against COVID-19. The structures of the unliganded enzyme and its complexes with a number of inhibitors were determined by multiple research groups using different experimental approaches and conditions; the resulting structures span 13 different polymorphs representing seven space groups. The structures of the enzyme itself, all determined by molecular replacement, are highly similar, with the exception of one polymorph with a different inter-domain orientation. However, a number of complexes with bound inhibitors were found to pose significant problems. Some of these could be traced to faulty definitions of geometrical restraints for ligands and to the general problem of a lack of such information in the PDB depositions. Several problems with ligand definition in the PDB itself were also noted. In several cases extensive corrections to the models were necessary to adhere to the evidence of the electron-density maps. Taken together, this analysis of a large number of structures of a single, medically important protein, all determined within less than a year using modern experimental tools, should be useful in future studies of other systems of high interest to the biomedical community.

Controlled devitrification of vitreous samples for high-resolution single-particle cryo-EM reduces beam-induced motion in the critical early frames of a movie stack by a factor of approximately four., As cryo-EM approaches the physical resolution limits imposed by electron optics and radiation damage, it becomes increasingly urgent to address the issues that impede high-resolution structure determination of biological specimens. One of the persistent problems has been beam-induced movement, which occurs when the specimen is irradiated with high-energy electrons. Beam-induced movement results in image blurring and loss of high-resolution information. It is particularly severe for biological samples in unsupported thin films of vitreous water. By controlled devitrification of conventionally plunge-frozen samples, the suspended film of vitrified water was converted into cubic ice, a polycrystalline, mechanically stable solid. It is shown that compared with vitrified samples, devitrification reduces beam-induced movement in the first 5 e Å−2 of an exposure by a factor of ∼4, substantially enhancing the contribution of the initial, minimally damaged frames to a structure. A 3D apoferritin map reconstructed from the first frames of 20 000 particle images of devitrified samples resolved undamaged side chains. Devitrification of frozen-hydrated specimens helps to overcome beam-induced specimen motion in single-particle cryo-EM, as a further step towards realizing the full potential of cryo-EM for high-resolution structure determination.

A large enhancement (118%) of electric field-induced strain of KTa1−xNbxO3 is achieved by Mn doping. The intensified local heterogeneity and modified structural features yielded by Mn dopants are demonstrated to be responsible for improved piezoelectricity. The role of Mn doping in local structures and properties of KTa1−xNbxO3 crystals is revealed, providing a basis for material design and performance optimization., Ion doping, an effective way to modify the nature of materials, is beneficial for the improvement of material properties. Mn doping exhibits gain of piezoelectric properties in KTa1−xNbxO3 (KTN). However, the impact mechanism of Mn ions on properties remains unclear. Here, the effects of Mn doping on local heterogeneity and piezoelectric properties in KTN are studied. The electric field-induced strain of Mn-doped KTN is ∼0.25% at 10 kV cm−1, 118% higher than that of pristine KTN. Meanwhile, as a result of Mn doping, the dielectric permittivity was tripled and the ferroelectricity was modified. The changes in A1(2TO), B1 + E(3TO) and E(4TO) vibrations characterized by Raman spectra indicate increased local polarization, weak correlation of dipoles and distorted lattices in Mn-doped KTN, respectively. First-principles calculations demonstrate stronger local heterogeneity introduced by Mn dopants, which weakens the dipole correlations and reduces domain sizes. As a result, the decreased domain sizes, combined with the larger ratio of lattice parameters c and a of the Mn-contained portion, are responsible for the higher piezoelectricity. This work reveals the impact on properties of KTN from Mn dopants and the prominent role of local heterogeneity in improving piezoelectricity, being valuable for the optimization and design of material properties.

Restraints extracted from molecule-in-cluster optimizations of separate disorder components permit improved least-squares modelling of experimental crystal structures, and considering energy barriers alongside enthalpy differences further enables the distinguishing of disorder into static and dynamic., Distinguishing disorder into static and dynamic based on multi-temperature X-ray or neutron diffraction experiments is the current state of the art, but is only descriptive, not predictive. Here, several disordered structures are revisited from the Cambridge Crystallographic Data Center ‘drug subset’, the Cambridge Structural Database and own earlier work, where experimental intensities of Bragg diffraction data were available. Using the molecule-in-cluster approach, structures with distinguishable conformations were optimized separately, as extracted from available or generated disorder models of the respective disordered crystal structures. Re-combining these ‘archetype structures’ by restraining positional and constraining displacement parameters for conventional least-squares refinement, based on the optimized geometries, then often achieves a superior fit to the experimental diffraction data compared with relying on experimental information alone. It also simplifies and standardizes disorder refinement. Ten example structures were analysed. It is observed that energy differences between separate disorder conformations are usually within a small energy window of RT (T = crystallization temperature). Further computations classify disorder into static or dynamic, using single experiments performed at one single temperature, and this was achieved for propionamide.

Using a theoretical method which employs equilibration between the cohesive and destructive energies of a crystal, it is shown that protein layers of monomolecular thickness formed in pores can grow into macroscopic crystals. Experimental studies, stimulated from theoretical considerations, widen the palette of porous materials that can promote protein crystallization., The nucleation ability of pores is explained using the equilibration between the cohesive energy maintaining the integrity of a crystalline cluster and the destructive energy tending to tear it up. It is shown that to get 3D crystals it is vital to have 2D crystals nucleating in the pores first. By filling the pore orifice, the 2D crystal nuclei are more stable because their peripheries are protected from the destructive action of water molecules. Furthermore, the periphery of the 2D crystal is additionally stabilized as a result of its cohesion with the pore wall. The understanding provided by this study combining theory and experiment will facilitate the design of new nucleants.

The impact of tetragonal crystal symmetry on the two-dimensional (2D) confined polymer nanostructure is demonstrated. Our research shows that this chain packing defect in the tetragonal cell can be controlled to develop along the rod long axis in 2D confinement., The symmetry of polymer crystals greatly affects the optical, thermal con­ductivity and mechanical properties of the materials. Past studies have shown that the two-dimensional (2D) confined crystallization of polymer nanorods could produce anisotropic structures. However, few researchers have focused on understanding confined nanostructures from the perspective of crystal sym­metry. In this research, we demonstrate the molecular chain self-assembly of tetragonal crystals under cylindrical confinement. We specifically selected poly(4-methyl-1-pentene) (P4MP1) with a 41 or 72 helical conformation (usually crystallizing with a tetragonal lattice) as the model polymer. We found a coherent crystal branching of the tetragonal crystal in the P4MP1 nanorods. The unusual 45°- and 135°-{200} diffractions and the meridional 220 diffraction (from 45°-tilted crystals) have shown a uniform crystal branching between the a 1-axis crystals and the 45°-tilted crystals in the rod long axis, which originates from a structural defect associated with tetragonal symmetry. Surprisingly, this chain packing defect in the tetragonal cell can be controlled to develop along the rod long axis in 2D confinement.

Competitive cocrystallization provides a green chemical method for flavonoid separation with fewer steps and lower energy consumption than the traditional organic solvent extraction method., Recently, cocrystallization has been widely employed to tailor physicochemical properties of drugs in the pharmaceutical field. In this study, cocrystallization was applied to separate natural compounds with similar structures. Three flavonoids [baicalein (BAI), quercetin (QUE) and myricetin (MYR)] were used as model compounds. The coformer caffeine (CAF) could form cocrystals with all three flavonoids, namely BAI–CAF (cocrystal 1), QUE–CAF (cocrystal 2) and MYR–CAF (cocrystal 3). After adding CAF to methanol solution containing MYR and QUE (or QUE and BAI), cocrystal 3 (or cocrystal 2) preferentially formed rather than cocrystal 2 (or cocrystal 1), indicating that flavonoid separation could be achieved by competitive cocrystallization. After co-mixing the slurry of two flavonoids with CAF followed by centrifugation, the resolution ratio that could be achieved was 70–80% with purity >90%. Among the three cocrystals, cocrystal 3 showed the lowest formation constant with a negative Gibbs free energy of nucleation and the highest energy gap. Hirshfeld surface analysis and density of states analysis found that cocrystal 3 had the highest strong interaction contribution and the closest electronic density, respectively, followed by cocrystal 2 and cocrystal 1, suggesting CAF could competitively form a cocrystal with MYR much more easily than QUE and BAI. Cocrystallization is a promising approach for green and effective separation of natural products with similar chemical structures.