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This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal–organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe—O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R1 reductions occurred in the low-resolution region (8.65–2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00–0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal–organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.

Chiral inorganic materials have attracted great attention owning to their unique physical and chemical properties attributed to the symmetry-breaking of their nanostructures. Chiral inorganic materials can be endowed with chiral geometric configurations from achiral space group crystals through lattice twisting, screw dislocations or hierarchical self-assembled spiral morphologies, showing various characteristic chiral anisotropy. However, the multilevel chirality in chiral nickel molybdate films (CNMFs) remains to be elaborately excavated. In this paper, we report three hierarchical levels of chirality in CNMFs, spanning from the atomic to the micron scale, including primary helically coiled nanoflakes with twisted atomic crystal lattices, secondary helical stacking of layered nanoflakes, and tertiary asymmetric morphology between adjacent nanoparticles. Our findings may enrich the chiral self-assembly structural types and provide valuable insights for the comprehensive analysis path of hierarchical chiral crystals. [ABSTRACT FROM AUTHOR]

Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235–244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740–751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92–109; Jha et al. (2021). J. Appl. Cryst. 54, 1234–1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment.

As one of the most stunning biological nanostructures, the single-diamond (SD) surface discovered in beetles and weevils exoskeletons possesses the widest complete photonic bandgap known to date and is renowned as the "holy grail" of photonic materials. However, the synthesis of SD is difficult due to its thermodynamical instability compared to the energetically favoured bicontinuous double diamond and other easily formed lattices; thus, the artificial fabrication of SD has long been a formidable challenge. Herein, we report a bottom-up approach to fabricate SD titania networks via a one-pot cooperative assembly scenario employing the diblock copolymer poly(ethylene oxide)-block-polystyrene as a soft template and titanium diisopropoxide bis(acetylacetonate) as an inorganic precursor in a mixed solvent, in which the SD scaffold was obtained by kinetically controlled nucleation and growth in the skeletal channels of the diamond minimal surface formed by the polymer matrix. Electron crystallography investigations revealed the formation of tetrahedrally connected SD frameworks with the space group Fd 3 m in a polycrystalline anatase form. A photonic bandgap calculation showed that the resulting SD structure has a wide and complete bandgap. This work solves the complex synthetic enigmas and offers a frontier in hyperbolic surfaces, biorelevant materials, next-generation optical devices, etc. [ABSTRACT FROM AUTHOR]

This work presents observations of symmetry breakages in the intensity distributions of near‐zone‐axis convergent‐beam electron diffraction (CBED) patterns that can only be explained by the symmetry of the specimen and not the symmetry of the unit cell describing the atomic structure of the material. The specimen is an aluminium–copper–tin alloy containing voids many tens of nanometres in size within continuous single crystals of the aluminium host matrix. Several CBED patterns where the incident beam enters and exits parallel void facets without the incident beam being perpendicular to these facets are examined. The symmetries in their intensity distributions are explained by the specimen morphology alone using a geometric argument based on the multislice theory. This work shows that it is possible to deduce nanoscale morphological information about the specimen in the direction of the electron beam – the elusive third dimension in transmission electron microscopy – from the inspection of CBED patterns. [ABSTRACT FROM AUTHOR]

Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein–protein contacts but also due to increased lipid–protein complementarity. Since each tetramer interacts with four such ‘glue’ cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts.

Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.

Over 30 years ago, it was shown that bonding between atoms has a noticeable effect on convergent beam electron diffraction patterns. The paper by Olech et al. [(2024). IUCrJ, 11, 309–324] demonstrates that its influence is also clearly present in 3D electron diffraction data, opening up new possibilities for quantum crystallography.

The resolution of 3D electron diffraction (ED) data of small‐molecule crystals is often relatively poor, due to either electron‐beam radiation damage during data collection or poor crystallinity of the material. Direct methods, used as standard for crystal structure determination, are not applicable when the data resolution falls below the commonly accepted limit of 1.2 Å. Therefore an evaluation was carried out of the performance of molecular replacement (MR) procedures, regularly used for protein structure determination, for structure analysis of small‐molecule crystal structures from 3D ED data. In the course of this study, two crystal structures of Bi‐3812, a highly potent inhibitor of the oncogenic transcription factor BCL6, were determined: the structure of α‐Bi‐3812 was determined from single‐crystal X‐ray data, the structure of β‐Bi‐3812 from 3D ED data, using direct methods in both cases. These data were subsequently used for MR with different data types, varying the data resolution limit (1, 1.5 and 2 Å) and by using search models consisting of connected or disconnected fragments of BI‐3812. MR was successful with 3D ED data at 2 Å resolution using a search model that represented 74% of the complete molecule. [ABSTRACT FROM AUTHOR]

Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.

Mixed‐anion compounds widen the chemical space of attainable materials compared to single anionic compounds, but the exploration of their structural diversity is limited by common synthetic paths. Especially, oxychlorides rely mainly on layered structures, which suffer from low stability during photo(electro)catalytic processes. Herein we report a strategy to design a new polar 3D tetrahedral framework with composition Zn4Si2O7Cl2. We use a molten salt medium to enable low temperature crystallization of nanowires of this new compound, by relying on tetrahedral building units present in the melt to build the connectivity of the oxychloride. These units are combined with silicon‐based connectors from a non‐oxidic Zintl phase to enable precise tuning of the oxygen content. This structure brings high chemical and thermal stability, as well as strongly anisotropic hole mobility along the polar axis. These features, associated with the ability to adjust the transport properties by doping, enable to tune water splitting properties for photoelectrocatalytic H2 evolution and water oxidation. This work then paves the way to a new family of mixed‐anion solids [ABSTRACT FROM AUTHOR]

The crystallographic study of two polymorphs of the industrial pyrazolone Pigment Orange 13 (P.O.13) is reported. The crystal structure of the β phase was determined using single‐crystal X‐ray analysis of a tiny needle. The α phase was investigated using three‐dimensional electron diffraction. The electron diffraction data contain sharp Bragg reflections and strong diffuse streaks, associated with severe stacking disorder. The structure was solved by careful analysis of the diffuse scattering, and similarities of the unit‐cell parameters with the β phase. The structure solution is described in detail and this provides a didactic example of solving molecular crystal structures in the presence of diffuse scattering. Several structural models were constructed and optimized by lattice‐energy minimization with dispersion‐corrected DFT. A four‐layer model was found, which matches the electron diffraction data, including the diffuse scattering, and agrees with X‐ray powder data. Additionally, five further phases of P.O.13 are described. [ABSTRACT FROM AUTHOR]

The crystallographic study of two polymorphs of the industrial pyrazolone Pigment Orange 13 (P.O.13) is reported. The crystal structure of the β phase was determined using single‐crystal X‐ray analysis of a tiny needle. The α phase was investigated using three‐dimensional electron diffraction. The electron diffraction data contain sharp Bragg reflections and strong diffuse streaks, associated with severe stacking disorder. The structure was solved by careful analysis of the diffuse scattering, and similarities of the unit‐cell parameters with the β phase. The structure solution is described in detail and this provides a didactic example of solving molecular crystal structures in the presence of diffuse scattering. Several structural models were constructed and optimized by lattice‐energy minimization with dispersion‐corrected DFT. A four‐layer model was found, which matches the electron diffraction data, including the diffuse scattering, and agrees with X‐ray powder data. Additionally, five further phases of P.O.13 are described. [ABSTRACT FROM AUTHOR]

Microcrystal electron diffraction (MicroED) leverages the strong interaction between matter and electrons to determine protein structures from vanishingly small crystals. This strong interaction limits the thickness of crystals that can be investigated by MicroED, mainly due to absorption. Recent studies have demonstrated that focused ion-beam (FIB) milling can thin crystals into ideal-sized lamellae; however, it is not clear how to best apply FIB milling for MicroED. Here, the effects of polishing the lamellae, whereby the last few nanometers are milled away using a low-current gallium beam, are explored in both the platinum-precoated and uncoated samples. Our results suggest that precoating samples with a thin layer of platinum followed by polishing the crystal surfaces prior to data collection consistently led to superior results as indicated by higher signal-to-noise ratio, higher resolution, and better refinement statistics. This study lays the foundation for routine and reproducible methodology for sample preparation in MicroED.

Microcrystal electron diffraction (MicroED) allows for macromolecular structure solution from nanocrystals. To create crystals of suitable size for MicroED data collection, sample preparation typically involves sonication or pipetting a slurry of crystals from a crystallization drop. The resultant crystal fragments are fragile and the quality of the data that can be obtained from them is sensitive to subsequent sample preparation for cryoelectron microscopy as interactions in the water-air interface can damage crystals during blotting. Here, we demonstrate the use of a focused ion beam to generate lamellae of macromolecular protein crystals for continuous rotation MicroED that are of ideal thickness, easy to locate, and require no blotting optimization. In this manner, crystals of nearly any size may be scooped and milled to desired dimensions prior to data collection, thus streamlining the methodology for sample preparation for MicroED.

The ice-nucleation protein InaZ from Pseudomonas syringae contains a large number of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. Ab initio structures of this repeat segment, resolved to 1.1 Å by microfocus X-ray crystallography and to 0.9 Å by the cryo-EM method MicroED, were determined from both racemic and homochiral crystals. The benefits of racemic protein crystals for structure determination by MicroED were evaluated and it was confirmed that the phase restriction introduced by crystal centrosymmetry increases the number of successful trials during the ab initio phasing of the electron diffraction data. Both homochiral and racemic GSTSTA form amyloid-like protofibrils with labile, corrugated antiparallel β-sheets that mate face to back. The racemic GSTSTA protofibril represents a new class of amyloid assembly in which all-left-handed sheets mate with their all-right-handed counterparts. This determination of racemic amyloid assemblies by MicroED reveals complex amyloid architectures and illustrates the racemic advantage in macromolecular crystallography, now with submicrometre-sized crystals.

Micro-crystal electron diffraction (MicroED) combines the efficiency of electron scattering with diffraction to allow structure determination from nano-sized crystalline samples in cryoelectron microscopy (cryo-EM). It has been used to solve structures of a diverse set of biomolecules and materials, in some cases to sub-atomic resolution. However, little is known about the damaging effects of the electron beam on samples during such measurements. We assess global and site-specific damage from electron radiation on nanocrystals of proteinase K and of a prion hepta-peptide and find that the dynamics of electron-induced damage follow well-established trends observed in X-ray crystallography. Metal ions are perturbed, disulfide bonds are broken, and acidic side chains are decarboxylated while the diffracted intensities decay exponentially with increasing exposure. A better understanding of radiation damage in MicroED improves our assessment and processing of all types of cryo-EM data.

Electron crystallography is widespread in material science applications, but for biological samples its use has been restricted to a handful of examples where two-dimensional (2D) crystals or helical samples were studied either by electron diffraction and/or imaging. Electron crystallography in cryoEM, was developed in the mid-1970s and used to solve the structure of several membrane proteins and some soluble proteins. In 2013, a new method for cryoEM was unveiled and named Micro-crystal Electron Diffraction, or MicroED, which is essentially three-dimensional (3D) electron crystallography of microscopic crystals. This method uses truly 3D crystals, that are about a billion times smaller than those typically used for X-ray crystallography, for electron diffraction studies. There are several important differences and some similarities between electron crystallography of 2D crystals and MicroED. In this review, we describe the development of these techniques, their similarities and differences, and offer our opinion of future directions in both fields.

The gallium(III) nitridophosphate‐oxide Ga16/3[P12N24]O2 was synthesized by metathesis reaction between GaF3 and LiPN2. The crystal structure was elucidated by electron crystallography and powder X‐ray diffraction, comparing both approaches. This reveals a partially collapsed sodalite‐type structure (space group I4‾ ${\bar{4}}$ 3m, a=8.1585(2) Å) with a tilt angle ϕ of ∼33°. Vertex‐sharing PN4 tetrahedra build up a sodalite network that hosts gallium(III) cations and oxide anions. Gallium forms bonds to further three N atoms. The structure model is confirmed by EDX analyses, IR spectroscopy and bond valence sum calculations. [ABSTRACT FROM AUTHOR]

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement. [ABSTRACT FROM AUTHOR]

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide. [ABSTRACT FROM AUTHOR]

Nanomedicine is among the most fascinating areas of research. Most of the newly discovered pharmaceutical polymorphs, as well as many new synthesized or isolated natural products, appear only in form of nanocrystals. The development of techniques that allow investigating the atomic structure of nanocrystalline materials is therefore one of the most important frontiers of crystallography. Some unique features of electrons, like their non‐neutral charge and their strong interaction with matter, make this radiation suitable for imaging and detecting individual atoms, molecules, or nanoscale objects down to sub‐angstrom resolution. In the recent years the development of three‐dimensional (3D) electron diffraction (3D ED) has shown that electron diffraction can be successfully used to solve the crystal structure of nanocrystals and most of its limiting factors like dynamical scattering or limited completeness can be easily overcome. This article is a review of the state of the art of this method with a specific focus on how it can be applied to beam sensitive samples like small‐molecule organic nanocrystals. This article is categorized under:Therapeutic Approaches and Drug Discovery > Emerging Technologies [ABSTRACT FROM AUTHOR]

The complete crystal structures of two as-made zeolites with the ITQ-52 structure (IFW framework type), where an alkylphosphonium and an aminophosphonium dications have been used as their respective organic structure-directing agents, have been solved by three-dimensional electron diffraction. Both organic cations have also been located within the 10-ring that connects the cavities of the IFW framework using the diffraction data. [Display omitted] • Zeolite ITQ-52 can be obtained using different organic structure directing agents. • The location of the directing agent can be obtained using 3D electron diffraction. • Different diffraction techniques can be used depending on the samples. • Due to their resemblance, both organics locate in similar positions in the channels. • Changing the organic agent modifies the location of trivalent atoms in the zeolite. [ABSTRACT FROM AUTHOR]

The stable ϕ phase that forms below ∼923 K around the Al69.2Cu20.0Cr10.8 composition was found to be hexagonal [P63, a = 11.045 (2), c = 12.688 (2) Å] and isostructural to the earlier reported Al6.2Cu2Re X phase [Samuha, Grushko & Meshi (2016). J. Alloys Compd.670, 18–24]. Using the structural model of the latter, a successful Rietveld refinement of the XRD data for Al69.5Cu20.0Cr10.5 was performed. Both ϕ and X were found to be structurally related to the Al72.6Cu11.0Cr16.4 ζ phase [P63/m, a = 17.714, c = 12.591 Å; Sugiyama, Saito & Hiraga (2002). J. Alloys Compd.342, 148–152], with a close lattice parameter c and a τ‐times‐larger lattice parameter a (τ is the golden mean). The structural relationship between ζ and ϕ was established on the basis of the similarity of their layered structures and common features. Additionally, the strong‐reflections approach was successfully applied for the modeling of the ϕ phase based on the structural model of the ζ phase. The latter and the experimental structural model (retrieved following Rietveld refinement) were found to be essentially identical. [ABSTRACT FROM AUTHOR]

Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.

This study made use of a recently developed combination of advanced methods to reveal the atomic structure of a disordered nanocrystalline zeolite using exit wave reconstruction, automated diffraction tomography, disorder modelling and diffraction pattern simulation. By applying these methods, it was possible to determine the so far unknown structures of the hydrous layer silicate RUB-6 and the related zeolite-like material RUB-5. The structures of RUB-5 and RUB-6 contain the same dense layer-like building units (LLBUs). In the case of RUB-5, these building units are interconnected via additional SiO4/2 tetrahedra, giving rise to a framework structure with a 2D pore system consisting of intersecting 8-ring channels. In contrast, RUB-6 contains these LLBUs as separate silicate layers terminated by silanol/siloxy groups. Both RUB-6 and RUB-5 show stacking disorder with intergrowths of different polymorphs. The unique structure of RUB-6, together with the possibility for an interlayer expansion reaction to form RUB-5, make it a promising candidate for interlayer expansion with various metal sources to include catalytically active reaction centres.

Bicontinuous cubic structures in soft matter consist of two intertwining labyrinths separated by a partitioning layer. Combining experiments, numerical modelling and techniques in differential geometry, we investigate twinning defects in bicontinuous cubic structures. We first demonstrate that a twin boundary is most likely to occur at a plane that cuts the partitioning layer almost perpendicularly, so that the perturbation caused by twinning remains minimal. This principle can be used as a criterion to identify potential twin boundaries, as demonstrated through detailed investigations of mesoporous silica crystals characterized by diamond and gyroid surfaces. We then discuss that a twin boundary can result from a stacking fault in the arrangement of inter-lamellar attachments at an early stage of structure formation. It is further shown that enhanced curvature fluctuations near the twin boundary would cost energy because of geometrical frustration, which would be eased by a crystal distortion that is experimentally observed.

Aquaporin-0 (AQP0) tetramers form square arrays in lens membranes through a yet unknown mechanism, but lens membranes are enriched in sphingomyelin and cholesterol. Here, we determined electron crystallographic structures of AQP0 in sphingomyelin/cholesterol membranes and performed molecular dynamics (MD) simulations to establish that the observed cholesterol positions represent those seen around an isolated AQP0 tetramer and that the AQP0 tetramer largely defines the location and orientation of most of its associated cholesterol molecules. At a high concentration, cholesterol increases the hydrophobic thickness of the annular lipid shell around AQP0 tetramers, which may thus cluster to mitigate the resulting hydrophobic mismatch. Moreover, neighboring AQP0 tetramers sandwich a cholesterol deep in the center of the membrane. MD simulations show that the association of two AQP0 tetramers is necessary to maintain the deep cholesterol in its position and that the deep cholesterol increases the force required to laterally detach two AQP0 tetramers, not only due to protein-protein contacts but also due to increased lipid-protein complementarity. Since each tetramer interacts with four such 'glue' cholesterols, avidity effects may stabilize larger arrays. The principles proposed to drive AQP0 array formation could also underlie protein clustering in lipid rafts., Competing Interests: PC, JO, Bd, CA, TW No competing interests declared, (© 2023, Chiu, Orjuela et al.)

This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal-organic complex, iron(III) acetylacetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetylacetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe-O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe 3+ has a lower scattering amplitude than the Fe 3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R 1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R 1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe 3+ ), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R 1 reductions occurred in the low-resolution region (8.65-2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00-0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal-organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED., (open access.)

In this study, we successfully solve polymorphs A and B of zeolite EMM‐17, which can only crystallize in sub‐micrometer‐sized crystals while containing complex stacking disorders, from the three‐dimensional (3D) electron diffraction (ED) data. This is the first time that the atomic structure of this polymorph has been ab initio solved, and the result reveals a unique 10(12)×10(12)×11‐ring channel system. Moreover, we acquire the first atomic‐resolution images of EMM‐17 using integrated differential phase‐contrast scanning transmission electron microscopy. The images allow us to directly observe polymorphs B and C and discover a large number of local structural defects. Based on structural features unraveled from the reciprocal‐space 3D ED data and real‐space images, we propose a series of energetically feasible local structures in EMM‐17. We also demonstrate that the unique porous structure of EMM‐17 enables efficient kinetic separation of C6 alkane isomers. [ABSTRACT FROM AUTHOR]

Copper perchlorophthalocyanine (CuPcCl16, CuC32N8Cl16, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys.43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron‐sized crystals could be obtained. Three‐dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage‐tilt/beam‐tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit‐cell parameters were verified by Rietveld refinement from powder X‐ray diffraction data. The crystal structure was validated by many‐body dispersion density functional theory (DFT) calculations. CuPcCl16 crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972. [ABSTRACT FROM AUTHOR]

Recent advances in 3D electron diffraction have allowed the structure determination of several model proteins from submicrometric crystals, the unit-cell parameters and structures of which could be immediately validated by known models previously obtained by X-ray crystallography. Here, the first new protein structure determined by 3D electron diffraction data is presented: a previously unobserved polymorph of hen egg-white lysozyme. This form, with unit-cell parameters a = 31.9, b = 54.4, c = 71.8 Å, β = 98.8°, grows as needle-shaped submicrometric crystals simply by vapor diffusion starting from previously reported crystallization conditions. Remarkably, the data were collected using a low-dose stepwise experimental setup consisting of a precession-assisted nanobeam of ∼150 nm, which has never previously been applied for solving protein structures. The crystal structure was additionally validated using X-ray synchrotron-radiation sources by both powder diffraction and single-crystal micro-diffraction. 3D electron diffraction can be used for the structural characterization of submicrometric macromolecular crystals and is able to identify novel protein polymorphs that are hardly visible in conventional X-ray diffraction experiments. Additionally, the analysis, which was performed on both nanocrystals and microcrystals from the same crystallization drop, suggests that an integrated view from 3D electron diffraction and X-ray microfocus diffraction can be applied to obtain insights into the molecular dynamics during protein crystal growth.

The ice-nucleation protein InaZ from Pseudomonas syringae contains a large number of degenerate repeats that span more than a quarter of its sequence and include the segment GSTSTA. Ab initio structures of this repeat segment, resolved to 1.1 Å by microfocus X-ray crystallography and to 0.9 Å by the cryo-EM method MicroED, were determined from both racemic and homochiral crystals. The benefits of racemic protein crystals for structure determination by MicroED were evaluated and it was confirmed that the phase restriction introduced by crystal centrosymmetry increases the number of successful trials during the ab initio phasing of the electron diffraction data. Both homochiral and racemic GSTSTA form amyloid-like protofibrils with labile, corrugated antiparallel β-sheets that mate face to back. The racemic GSTSTA protofibril represents a new class of amyloid assembly in which all-left-handed sheets mate with their all-right-handed counterparts. This determination of racemic amyloid assemblies by MicroED reveals complex amyloid architectures and illustrates the racemic advantage in macromolecular crystallography, now with submicrometre-sized crystals.

We demonstrate that it is feasible to determine high-resolution protein structures by electron crystallography of three-dimensional crystals in an electron cryo-microscope (CryoEM). Lysozyme microcrystals were frozen on an electron microscopy grid, and electron diffraction data collected to 1.7 Å resolution. We developed a data collection protocol to collect a full-tilt series in electron diffraction to atomic resolution. A single tilt series contains up to 90 individual diffraction patterns collected from a single crystal with tilt angle increment of 0.1-1° and a total accumulated electron dose less than 10 electrons per angstrom squared. We indexed the data from three crystals and used them for structure determination of lysozyme by molecular replacement followed by crystallographic refinement to 2.9 Å resolution. This proof of principle paves the way for the implementation of a new technique, which we name 'MicroED', that may have wide applicability in structural biology. DOI: http://dx.doi.org/10.7554/eLife.01345.001.

Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand‐binding interactions and (iv) determining membrane‐protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology. [ABSTRACT FROM AUTHOR]

Dynamical refinement is a well established method for refining crystal structures against 3D electron diffraction (ED) data and its benefits have been discussed in the literature [Palatinus, Petříček & Corrêa, (2015). Acta Cryst. A71, 235-244; Palatinus, Corrêa et al. (2015). Acta Cryst. B71, 740-751]. However, until now, dynamical refinements have only been conducted using the independent atom model (IAM). Recent research has shown that a more accurate description can be achieved by applying the transferable aspherical atom model (TAAM), but this has been limited only to kinematical refinements [Gruza et al. (2020). Acta Cryst. A76, 92-109; Jha et al. (2021). J. Appl. Cryst. 54, 1234-1243]. In this study, we combine dynamical refinement with TAAM for the crystal structure of 1-methyluracil, using data from precession ED. Our results show that this approach improves the residual Fourier electrostatic potential and refinement figures of merit. Furthermore, it leads to systematic changes in the atomic displacement parameters of all atoms and the positions of hydrogen atoms. We found that the refinement results are sensitive to the parameters used in the TAAM modelling process. Though our results show that TAAM offers superior performance compared with IAM in all cases, they also show that TAAM parameters obtained by periodic DFT calculations on the refined structure are superior to the TAAM parameters from the UBDB/MATTS database. It appears that multipolar parameters transferred from the database may not be sufficiently accurate to provide a satisfactory description of all details of the electrostatic potential probed by the 3D ED experiment., (open access.)

Over 30 years ago, it was shown that bonding between atoms has a noticeable effect on convergent beam electron diffraction patterns. The paper by Olech et al. [(2024). IUCrJ, 11, 309-324] demonstrates that its influence is also clearly present in 3D electron diffraction data, opening up new possibilities for quantum crystallography., (open access.)

As one of the most stunning biological nanostructures, the single-diamond (SD) surface discovered in beetles and weevils exoskeletons possesses the widest complete photonic bandgap known to date and is renowned as the "holy grail" of photonic materials. However, the synthesis of SD is difficult due to its thermodynamical instability compared to the energetically favoured bicontinuous double diamond and other easily formed lattices; thus, the artificial fabrication of SD has long been a formidable challenge. Herein, we report a bottom-up approach to fabricate SD titania networks via a one-pot cooperative assembly scenario employing the diblock copolymer poly(ethylene oxide)- block -polystyrene as a soft template and titanium diisopropoxide bis(acetylacetonate) as an inorganic precursor in a mixed solvent, in which the SD scaffold was obtained by kinetically controlled nucleation and growth in the skeletal channels of the diamond minimal surface formed by the polymer matrix. Electron crystallography investigations revealed the formation of tetrahedrally connected SD frameworks with the space group Fd [Formula: see text] m in a polycrystalline anatase form. A photonic bandgap calculation showed that the resulting SD structure has a wide and complete bandgap. This work solves the complex synthetic enigmas and offers a frontier in hyperbolic surfaces, biorelevant materials, next-generation optical devices, etc., Competing Interests: Competing interests statement:The authors declare no competing interest.

There is a wealth of materials that are beam sensitive and only exist in nanometric crystals, because the growth of bigger crystals is either impossible or so complicated that it is not reasonable to spend enough time and resources to grow big crystals before knowing their potential for research or applications. This difficulty is encountered in minerals, zeolites, metal-organic frameworks or molecular crystals, including pharmaceuticals and biological crystals. In order to study these crystals a structure determination method for beam sensitive crystals of nanometric size is needed. The nanometric size makes them destined for electron diffraction, since electrons interact much more strongly with matter than X-rays or neutrons. In addition, for the same amount of beam damage, electron diffraction yields more information than X-rays. The recently developed low-dose electron diffraction tomography (LD-EDT) not only combines the advantages inherent in electron diffraction, but is also optimized for minimizing the electron dose used for the data collection. The data quality is high, allowing not only the solution of complex unknown structures, but also their refinement taking into account the dynamical diffraction effects. Here we present several examples of crystals solved and refined by this method. The range of the crystals presented includes two synthetic oxides, Sr5CuGe9O24 and (Na2/3Mn1/3)3Ge5O12, a natural mineral (bulachite), and a metal organic framework (Mn-formiate). The dynamical refinement can be successfully performed on data sets that needed less than 0.1 e−/Å2 for the entire data set.

Abstract We present new transmission electron microscopy (TEM) based electron diffraction characterization techniques (orientation imaging combined with 3D precession electron diffraction tomography-ADT) applied on cultural heritage materials. We have determined precisely unit cell parameters, crystal symmetry, atomic structure, and orientation/phase mapping of various pigment/opacifier crystallites at nm scale which are present in green and white Roman glass tesserae. Such TEM techniques can be an alternative to Synchrotron based techniques, and allow to distinguish accurately at nm scale between different crystal structures even in cases of same/very close chemical composition, where is also possible to visualize between different crystal orientations and amorphous/crystalline phases. This study additionally demonstrates that although opacifiers in green and white tesserae are found to have average Pb2Sb2O7 cubic and CaSb2O6 trigonal structures, their pyrochlore related framework can host many other elements like Cu, Ca, Fe through ionic exchanges at high firing temperatures which in turn may also contribute to the tesserae colour appearance.

Ionic scattering factors of atoms that compose biological molecules have been computed by the multi-configuration Dirac–Fock method. These ions are chemically unstable and their scattering factors had not been reported except for O−. Yet these factors are required for the estimation of partial charges in protein molecules and nucleic acids. The electron scattering factors of these ions are particularly important as the electron scattering curves vary considerably between neutral and charged atoms in the spatial-resolution range explored in structural biology. The calculated X-ray and electron scattering factors have then been parameterized for the major scattering curve models used in X-ray and electron protein crystallography and single-particle cryo-EM. The X-ray and electron scattering factors and the fitting parameters are presented for future reference.

Electron crystallography is a discipline that currently attracts much attention as method for inorganic, organic and macromolecular structure solution. EIGER, a direct-detection hybrid pixel detector developed at the Paul Scherrer Institut, Switzerland, has been tested for electron diffraction in a transmission electron microscope. EIGER features a pixel pitch of 75 × 75 µm2, frame rates up to 23 kHz and a dead time between frames as low as 3 µs. Cluster size and modulation transfer functions of the detector at 100, 200 and 300 keV electron energies are reported and the data quality is demonstrated by structure determination of a SAPO-34 zeotype from electron diffraction data.

Microcrystal electron diffraction (MicroED) has recently shown to be a promising technique for structure determination in structural biology and pharmaceutical chemistry. Here, we discuss the unique properties of electrons and motivate its use for diffraction experiments. We review the latest developments in MicroED, and illustrate its applications in macromolecular crystallography, fragment screening and structure guided drug discovery. We discuss the perspectives of MicroED in synthetic chemistry and pharmaceutical development. We anticipate that the rapid advances MicroED showcased here will promote further development of electron crystallography and open up new opportunities for drug discovery. [ABSTRACT FROM AUTHOR]

In the framework of expanding the range of copper‐based compounds in the pyroxene family, we have synthesized at high pressure and high temperature a powder containing a mixture of a new phase with stoichiometry Sr5CuGe9O24 having two identified impurity phases. Electron crystallography showed that the new phase crystallizes in the monoclinic space group P2/c, with unit‐cell parameters a = 11.8 Å, b = 8.1 Å, c = 10.3 Å and β = 101.3°. We applied the recently developed low‐dose electron diffraction tomography method to solve the structure by direct methods. The obtained structure model contains all 9 independent cation positions and all 13 oxygen positions. A subsequent refinement against powder X‐ray diffraction data ascertained the high quality of the structure solution, in particular, the unusual structural arrangement that there are three different environments for Ge in this phase. [ABSTRACT FROM AUTHOR]

A revolution in resolution is occurring now in electron microscopy arising from the development of methods for imaging single particles at cryogenic temperatures and obtaining electron diffraction data from nanocrystals of small organic molecules or macromolecules. Near‐atomic or even atomic resolution of molecular structures can be achieved. The basis of these methods is the scattering of an electron beam due to the electrostatic potential of the sample. To analyse these high‐quality experimental data, it is necessary to use appropriate atomic scattering factors. The independent atom model (IAM) is commonly used although various more advanced models, already known from X‐ray diffraction, can also be applied to enhance the analysis. In this study a comparison is presented of IAM and TAAM (transferable aspherical atom model), the latter with the parameters of the Hansen–Coppens multipole model transferred from the University at Buffalo Databank (UBDB). By this method, TAAM takes into account the fact that atoms in molecules are partially charged and are not spherical. Structure refinements were performed on a carbamazepine crystal using electron structure‐factor amplitudes determined experimentally [Jones et al. (2018). ACS Cent. Sci.4, 1587–1592] or modelled with theoretical quantum‐mechanical methods. The results show the possibilities and limitations of the TAAM method when applied to electron diffraction. Among others, the method clearly improves model fitting statistics, when compared with IAM, and allows for reliable refinement of atomic thermal parameters. The improvements are more pronounced with poorer‐resolution diffraction data. [ABSTRACT FROM AUTHOR]