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The authors study the effect of changes in the transparency of magnetic emulsions with deformable droplets of submicrometer size under the influence of magnetic field. The effect the orientation and strength of the magnetic field and the concentration of microdroplets have on the amplitude of transparency changes is revealed. Experimental data on the field dependence of the magneto-optical effect and its dependence on the angle of the magnetic field's orientation are compared via calculations in an approximation of anomalous diffraction. The possibility of determining interphase tension in magnetic emulsions is analyzed by studying the relaxation of optical effects. [ABSTRACT FROM AUTHOR]

The evolution of the uranium chemical state in uranium compounds, principally in the oxides, is of concern in the context of nuclear fuel degradation under storage and repository conditions, and in accident scenarios. The U–O system shows complicated phase relations between single‐valence uranium dioxide (UO2) and different mixed‐valence compounds (e.g. U4O9, U3O7 and U3O8). To try resolving the electronic structure associated with unique atomic positions, a combined application of diffraction and spectroscopic techniques, such as diffraction anomalous fine structure (DAFS), can be considered. Reported here is the application of two newly developed routines for assessing a DAFS data set, with the aim of refining the uranium X‐ray dispersion corrections. High‐resolution anomalous diffraction data were acquired from polycrystalline powder samples of UO2 (containing tetravalent uranium) and potassium uranate (KUO3, containing pentavalent uranium) using synchrotron radiation in the vicinity of the U L3 edge (17.17 keV). Both routines are based on an iterative refinement of the dispersion corrections, but they differ in either using the intensity of a selection of reflections or doing a full‐pattern (Rietveld method) refinement. The uranium dispersion corrections obtained using either method are in excellent agreement with each other, and they show in great detail the chemical shifts and differences in fine structure expected for tetravalent and pentavalent uranium. This approach may open new possibilities for the assessment of other, more complicated, materials such as mixed‐valence compounds. Additionally, the DAFS methodology can offer a significant resource optimization because each data set contains both structural (diffraction) and chemical (spectroscopy) information, which can avoid the requirement to use multiple experimental stations at synchrotron sources. [ABSTRACT FROM AUTHOR]

The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. Since these patterns record only amplitudes, phases for the diffracted waves must also be evaluated for systematic structure determination. Thus, we have the phase problem as a central complication, both intellectually for the field and practically so for many analyses. Here, I discuss how we – myself, my laboratory and the diffraction community – have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. During the explosive growth of macromolecular crystallography, practice in diffraction analysis evolved from a universal reliance on isomorphous replacement to the eventual domination of anomalous diffraction for de novo structure determination. As the Protein Data Bank (PDB) grew and familial relationships among proteins became clear, molecular replacement overtook all other phasing methods; however, experimental phasing remained essential for molecules without obvious precedents, with multi- and single-wavelength anomalous diffraction (MAD and SAD) predominating. While the mathematics-based direct methods had proved to be inadequate for typical macromolecules, they returned to crack substantial selenium substructures in SAD analyses of selenomethionyl proteins. Native SAD, exploiting the intrinsic S and P atoms of biomolecules, has become routine. Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. Currently, molecular replacement with AlphaFold models often obviates the need for experimental phase evaluation. For multiple reasons, we are now unfazed by the phase problem. Cryo-EM analysis is an attractive alternative to crystallography for many applications faced by today's structural biologists. It simply finesses the phase problem; however, the principles and procedures of diffraction analysis remain pertinent and are adopted in single-particle cryo-EM studies of biomolecules.

The features of the magneto-optical effect of optical density change in magnetic emulsions with low interfacial tension, synthesized on the basis of kerosene magnetic fluid and AMG-10 oil, are studied. It is shown that the magnitude and sign of the effect essentially depend on the size of the emulsion droplets. The effect is interpreted on the basis of the anomalous diffraction approximation, and a method is proposed for estimating the size of magnetic emulsion microdroplets depending on the sign of the magneto-optical effect in longitudinal and transverse magnetic fields. [ABSTRACT FROM AUTHOR]

Understanding the electronic structures of high‐valent metal complexes aids the advancement of metal‐catalyzed cross coupling methodologies. A prototypical complex with formally high valency is [Cu(CF3)4]− (1), which has a formal Cu(III) oxidation state but whose physical analysis has led some to a Cu(I) assignment in an inverted ligand field model. Recent examinations of 1 by X‐ray spectroscopies have led previous authors to contradictory conclusions, motivating the re‐examination of its X‐ray absorption profile here by a complementary method, resonant diffraction anomalous fine structure (DAFS). From analysis of DAFS measurements for a series of seven mononuclear Cu complexes including 1, here it is shown that there is a systematic trifluoromethyl effect on X‐ray absorption that blue shifts the resonant Cu K‐edge energy by 2–3 eV per CF3, completely accounting for observed changes in DAFS profiles between formally Cu(III) complexes like 1 and formally Cu(I) complexes like (Ph3P)3CuCF3 (3). Thus, in agreement with the inverted ligand field model, the data presented herein imply that 1 is best described as containing a Cu(I) ion with dn count approaching 10. [ABSTRACT FROM AUTHOR]

De novo structure determination from single-wavelength anomalous diffraction using native sulfur or phosphorus in biomolecules (native-SAD) is an appealing method to mitigate the labor-intensive production of heavy-atom derivatives and selenomethionyl substitutions. The native-SAD method is particularly attractive for membrane proteins, which are difficult to produce and often recalcitrant to grow into decent-sized crystals. Native-SAD uses lower-energy X-rays to enhance anomalous signals from sulfur or phosphorus. However, at lower energies, the scattering and absorption of air contribute to the background noise, reduce the signals and are thus adverse to native-SAD phasing. We have previously demonstrated native-SAD phasing at an energy of 5 keV in air at the NSLS-II FMX beamline. Here, the use of a helium path developed to reduce both the noise from background scattering and the air absorption of the diffracted X-ray beam are described. The helium path was used for collection of anomalous diffraction data at 5 keV for two proteins: thaumatin and the membrane protein TehA. Although anomalous signals from each individual crystal are very weak, robust anomalous signals are obtained from data assembled from micrometre-sized crystals. The thaumatin structure was determined from 15 microcrystals and the TehA structure from 18 microcrystals. These results demonstrate the usefulness of a helium environment in support of native-SAD phasing at 5 keV.

X‐ray crystallography has been invaluable in delivering structural information about proteins. Previously, an approach has been developed that allows high‐quality X‐ray diffraction data to be obtained from protein crystals at and above room temperature. Here, this previous work is built on and extended by showing that high‐quality anomalous signal can be obtained from single protein crystals using diffraction data collected at 220 K up to physiological temperatures. The anomalous signal can be used to directly determine the structure of a protein, i.e. to phase the data, as is routinely performed under cryoconditions. This ability is demonstrated by obtaining diffraction data from model lysozyme, thaumatin and proteinase K crystals, the anomalous signal from which allowed their structures to be solved experimentally at 7.1 keV X‐ray energy and at room temperature with relatively low data redundancy. It is also demonstrated that the anomalous signal from diffraction data obtained at 310 K (37°C) can be used to solve the structure of proteinase K and to identify ordered ions. The method provides useful anomalous signal at temperatures down to 220 K, resulting in an extended crystal lifetime and increased data redundancy. Finally, we show that useful anomalous signal can be obtained at room temperature using X‐rays of 12 keV energy as typically used for routine data collection, allowing this type of experiment to be carried out at widely accessible synchrotron beamline energies and enabling the simultaneous extraction of high‐resolution data and anomalous signal. With the recent emphasis on obtaining conformational ensemble information for proteins, the high resolution of the data allows such ensembles to be built, while the anomalous signal allows the structure to be experimentally solved, ions to be identified, and water molecules and ions to be differentiated. Because bound metal‐, phosphorus‐ and sulfur‐containing ions all have anomalous signal, obtaining anomalous signal across temperatures and up to physiological temperatures will provide a more complete description of protein conformational ensembles, function and energetics. [ABSTRACT FROM AUTHOR]

Na+ is the most abundant ion in living organisms and plays essential roles in regulating nutrient uptake, muscle contraction, and neurotransmission. The identification of Na+ in protein structures is crucial for gaining a deeper understanding of protein function in a physiological context. LeuT, a bacterial homolog of the neurotransmitter:sodium symporter family, uses the Na+ gradient to power the uptake of amino acids into cells and has been used as a paradigm for the study of Na+-dependent transport systems. We have devised a low-energy multi-crystal approach for characterizing low-Z (Z ≤ 20) anomalous scattering ions such as Na+, Mg2+, K+, and Ca2+ by combining Bijvoet-difference Fourier syntheses for ion detection and f" refinements for ion speciation. Using the approach, we experimentally identify two Na+ bound near the central leucine binding site in LeuT. Using LeuT microcrystals, we also demonstrate that Na+ may be depleted to study conformational changes in the LeuT transport cycle. [ABSTRACT FROM AUTHOR]

A commentary on Wayne Hendrickson's article `Facing the phase problem'.

Heteroduplexes composed of all-DNA and all-2′-OMe RNA strands do not occur in nature, but they have found application in the development of molecular beacons and could also be used as aptamers or elements of nucleic acid-based nanostructures that will contain such structural motifs. The crystallization experiments performed have shown that the introduction of overhangs at the ends of the duplex has a great influence on the success of crystallization, as well as on the DNA:2′-OMe-RNA heteroduplex crystal packing. The molecular and crystal structure of the DNA:2′-O-methyl-RNA heteroduplex in its overhanging and blunt-ended versions was determined at 100 K using synchrotron radiation with a resolution of 1.91 and 1.55 Å, respectively. The Zn-SAD method was used to resolve the original duplex structure when molecular replacement by many existing models of duplex structures failed. Both molecules analyzed adopted a conformation close to the A-RNA double helix. The presented structures provide the first insight into this type of heteroduplexes and allowed a comparative analysis with existing nucleic acid homo- and heteroduplex structures. The results of our research expand the knowledge of the structural properties of new heteroduplexes and may be useful for future applications, such as therapies using this class of compounds. [ABSTRACT FROM AUTHOR]

Na+ is the most abundant ion in living organisms and plays essential roles in regulating nutrient uptake, muscle contraction, and neurotransmission. The identification of Na+ in protein structures is crucial for gaining a deeper understanding of protein function in a physiological context. LeuT, a bacterial homolog of the neurotransmitter:sodium symporter family, uses the Na+ gradient to power the uptake of amino acids into cells and has been used as a paradigm for the study of Na+-dependent transport systems. We have devised a low-energy multi-crystal approach for characterizing low-Z (Z ≤ 20) anomalous scattering ions such as Na+, Mg2+, K+, and Ca2+ by combining Bijvoet-difference Fourier syntheses for ion detection and f” refinements for ion speciation. Using the approach, we experimentally identify two Na+ bound near the central leucine binding site in LeuT. Using LeuT microcrystals, we also demonstrate that Na+ may be depleted to study conformational changes in the LeuT transport cycle.

Specific features of the magneto-optical effect of a change in the transparency of a magnetic emulsion with low interfacial tension have been investigated. The effect has been interpreted within the anomalous diffraction approximation. The characteristic times of field action, at which the processes of sample coalescence and structuring do not affect the optical effect, are determined. The effect relaxation time is found and the data obtained are compared with the results of calculations, performed according to the mechanisms of small deformation of microdroplets and Brownian rotational diffusion. [ABSTRACT FROM AUTHOR]

De novo structural evaluation of native biomolecules from single-wavelength anomalous diffraction (SAD) is a challenge because of the weakness of the anomalous scattering. The anomalous scattering from relevant native elements – primarily sulfur in proteins and phosphorus in nucleic acids – increases as the X-ray energy decreases toward their K-edge transitions. Thus, measurements at a lowered X-ray energy are promising for making native SAD routine and robust. For microcrystals with sizes less than 10 µm, native-SAD phasing at synchrotron microdiffraction beamlines is even more challenging because of difficulties in sample manipulation, diffraction data collection and data analysis. Native-SAD analysis from microcrystals by using X-ray free-electron lasers has been demonstrated but has required use of thousands of thousands of microcrystals to achieve the necessary accuracy. Here it is shown that by exploitation of anomalous microdiffraction signals obtained at 5 keV, by the use of polyimide wellmounts, and by an iterative crystal and frame-rejection method, microcrystal native-SAD phasing is possible from as few as about 1 200 crystals. Our results show the utility of low-energy native-SAD phasing with microcrystals at synchrotron microdiffraction beamlines.

Heteroduplexes composed of all-DNA and all-2′-OMe RNA strands do not occur in nature, but they have found application in the development of molecular beacons and could also be used as aptamers or elements of nucleic acid-based nanostructures that will contain such structural motifs. The crystallization experiments performed have shown that the introduction of overhangs at the ends of the duplex has a great influence on the success of crystallization, as well as on the DNA:2′-OMe-RNA heteroduplex crystal packing. The molecular and crystal structure of the DNA:2′-O-methyl-RNA heteroduplex in its overhanging and blunt-ended versions was determined at 100 K using synchrotron radiation with a resolution of 1.91 and 1.55 Å, respectively. The Zn-SAD method was used to resolve the original duplex structure when molecular replacement by many existing models of duplex structures failed. Both molecules analyzed adopted a conformation close to the A-RNA double helix. The presented structures provide the first insight into this type of heteroduplexes and allowed a comparative analysis with existing nucleic acid homo- and heteroduplex structures. The results of our research expand the knowledge of the structural properties of new heteroduplexes and may be useful for future applications, such as therapies using this class of compounds.

In the last few years, there is a huge upsurge in the number of closed deals regarding quantum technologies for materials, computing, communication and instrumentation. Such a trend has inevitably affected the research funding market; thus, large state initiatives are taken that are directly expected to drive the formulation of novel research concepts and the development of quantum device prototypes from sensors and circuitry to quantum memory and repeaters. A fundamental operation behind all these applications is the effective steering of electrons, constituting matter waves, along specific directions and with certain magnitudes, due to development of various reflective and refractive orders. The objective of this study is to optimize the simplest structure that supports such anomalous diffraction, namely a quantum metasurface comprising cylindrical rods embedded in suitable crystalline matter. Several highly-performing designs from these minimal setups are proven to work exceptionally as multiport components, employable to a variety of quantum engineering implementations. [ABSTRACT FROM AUTHOR]

Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order–disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X‐ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f′ and f′′ of the energy of the radiation, especially close to the element‐specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC‐2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X‐ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz‐kesterite structure type. [ABSTRACT FROM AUTHOR]

The focus of this work is on the relationship between the quantitative structural characterization of bimetallic Au-Pd nanoparticles dispersed in an amorphous polymer matrix and their catalytic activity in the direct synthesis of hydrogen peroxide (DS reaction). Resonant X-ray powder diffraction with synchrotron radiation was employed to probe selectively and to reveal fine details of the structure of bimetallic nanoparticles embedded in the support. The semi-quantitative analysis of the resonant X-ray powdered diffraction data, made on a large number of metal nanoparticles, shows that in one of the polymer-supported Au-Pd catalyst for the DS reaction (P75) featured by an overall molar Pd/Au of about 5.54, the smallest metal nanoparticles (MNPs), which account for more than 99.9% of the total MNPs number and for more than 95% of the metal surface, are formed by practically pure palladium. The relative number of bimetallic alloyed nanoparticles is very small (less than 4 × 102 ppm) and they contribute to only about 2% of the total metal surface. In a second gold-enriched catalyst (P50) with an overall molar Pd/Au of 1.84, the proportion of the bimetallic alloyed nanoparticles increased to about 97% and they account for about 99% of the metal surface. As a result of the metal intermixing, the catalytic productivity for the DS reaction increased from 97 to 109 mmolH2O2/molH2, owing to the gold-promotion of palladium. [ABSTRACT FROM AUTHOR]

RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (KD of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (KD of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research community.

Site occupancies in a single-phase σ-intermetallic compound of composition Cr 46 Mn 15.2 Fe 16.3 Co 17 Ni 5.5 (in at.%) were studied. To the best of the authors' knowledge, such a complex analysis with 5 elements occupying 5 different sites has never been tackled before and is addressed here using cutting edge X-ray diffraction techniques, absorption spectroscopy and simulations. Resonant powder diffraction data were collected at the K-edges of each of the five elements and the site occupancies were refined by a joint Rietveld analysis. Dispersion coefficients were retrieved independently from tabulated values, Kramers-Kronig relations and reference samples. Additional Extended X-ray Absorption Fine Structure (EXAFS) measurements were used to confirm the site occupancies and bond lengths. The site occupancies were independently obtained by a thermodynamic approach based on the enthalpies of formation of the 55 = 3125 configurations generated by the ordered distribution of the five components on the five sublattices, derived from a machine learning approach based on a DFT database. Overall, the calculations and experiments are in excellent agreement and reveal that the σ phase can accommodate a considerable degree of disorder, which consequences for thermodynamic modeling are discussed. The configurational entropy (S) of the σ phase represents 84% of that of a fully disordered alloy with the same composition, which is much larger than that expected for a fully ordered intermetallic phase (S = 0). The corresponding entropic stabilization is one of the reasons for the fact that the σ phase is one of the most important intermetallic that precipitates in high-entropy alloys and many engineering materials. Site occupancies of Cr, Mn, Fe, Co, and Ni on the five different sublattices of the quinary σ phase obtained from resonant diffraction experiment. [Display omitted] [ABSTRACT FROM AUTHOR]

Understanding the electronic structures of high-valent metal complexes aids the advancement of metal-catalyzed cross coupling methodologies. A prototypical complex with formally high valency is [Cu(CF 3 ) 4 ] - (1), which has a formal Cu(III) oxidation state but whose physical analysis has led some to a Cu(I) assignment in an inverted ligand field model. Recent examinations of 1 by X-ray spectroscopies have led previous authors to contradictory conclusions, motivating the re-examination of its X-ray absorption profile here by a complementary method, resonant diffraction anomalous fine structure (DAFS). From analysis of DAFS measurements for a series of seven mononuclear Cu complexes including 1, here it is shown that there is a systematic trifluoromethyl effect on X-ray absorption that blue shifts the resonant Cu K-edge energy by 2-3 eV per CF 3 , completely accounting for observed changes in DAFS profiles between formally Cu(III) complexes like 1 and formally Cu(I) complexes like (Ph 3 P) 3 CuCF 3 (3). Thus, in agreement with the inverted ligand field model, the data presented herein imply that 1 is best described as containing a Cu(I) ion with d n count approaching 10., (© 2023 Wiley-VCH GmbH.)

The focus of this work is on the relationship between the quantitative structural characterization of bimetallic Au-Pd nanoparticles dispersed in an amorphous polymer matrix and their catalytic activity in the direct synthesis of hydrogen peroxide (DS reaction). Resonant X-ray powder diffraction with synchrotron radiation was employed to probe selectively and to reveal fine details of the structure of bimetallic nanoparticles embedded in the support. The semi-quantitative analysis of the resonant X-ray powdered diffraction data, made on a large number of metal nanoparticles, shows that in one of the polymer-supported Au-Pd catalyst for the DS reaction (P75) featured by an overall molar Pd/Au of about 5.54, the smallest metal nanoparticles (MNPs), which account for more than 99.9% of the total MNPs number and for more than 95% of the metal surface, are formed by practically pure palladium. The relative number of bimetallic alloyed nanoparticles is very small (less than 4 × 102 ppm) and they contribute to only about 2% of the total metal surface. In a second gold-enriched catalyst (P50) with an overall molar Pd/Au of 1.84, the proportion of the bimetallic alloyed nanoparticles increased to about 97% and they account for about 99% of the metal surface. As a result of the metal intermixing, the catalytic productivity for the DS reaction increased from 97 to 109 mmolH2O2/molH2, owing to the gold-promotion of palladium.

Ferroelectric materials are used in actuators or sensors because of their non-volatile macroscopic electric polarization. GeTe is the simplest known diatomic ferroelectric endowed with exceedingly complex physics related to its crystalline, amorphous, thermoelectric, and—fairly recently discovered—topological properties, making the material potentially interesting for spintronics applications. Typically, ferroelectric materials possess random oriented domains that need poling to achieve macroscopic polarization. By using X-ray absorption fine structure spectroscopy complemented with anomalous diffraction and piezo-response force microscopy, we investigated the bulk ferroelectric structure of GeTe crystals and thin films. Both feature multi-domain structures in the form of oblique domains for films and domain colonies inside crystals. Despite these multi-domain structures which are expected to randomize the polarization direction, our experimental results show that at room temperature there is a preferential ferroelectric order remarkably consistent with theoretical predictions from ideal GeTe crystals. This robust self-poled state has high piezoelectricity and additional poling reveals persistent memory effects.

A method to calibrate and stabilize the incident X-ray energy for anomalous diffraction data collection is provided and has been successfully used at the single-crystal diffraction beamline 1W2B at the Beijing Synchrotron Radiation Facilities. Employing a feedback loop to control the movement of the double-crystal monochromator, this new method enables the incident X-ray energy to be kept within a 0.2 eV range at the inflection point of the absorption edge. [ABSTRACT FROM AUTHOR]

High-quality high-multiplicity X-ray diffraction data were collected on five different crystals of thaumatin using a homogeneous-profile X-ray beam at E = 8 keV to investigate the counteracting effects of increased multiplicity and increased radiation damage on the quality of anomalous diffraction data collected on macromolecular crystals. By comparing sulfur substructures obtained from subsets of the data selected as a function of absorbed X-ray dose with sulfur positions in the respective refined reference structures, the doses at which the highest quality of anomalous differences could be obtained were identified for the five crystals. A statistic σ{Δ F} D, calculated as the width σ of the normalized distribution of a set {Δ F} of anomalous differences collected at a dose D, is suggested as a measure of anomalous data quality as a function of dose. An empirical rule is proposed to identify the dose at which the gains in data quality due to increased multiplicity are outbalanced by the losses due to decreases in signal-to-noise as a consequence of radiation damage. Identifying this point of diminishing returns allows the optimization of the choice of data collection parameters and the selection of data to be used in subsequent crystal structure determination steps. [ABSTRACT FROM AUTHOR]

The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. Since these patterns record only amplitudes, phases for the diffracted waves must also be evaluated for systematic structure determination. Thus, we have the phase problem as a central complication, both intellectually for the field and practically so for many analyses. Here, I discuss how we - myself, my laboratory and the diffraction community - have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. During the explosive growth of macromolecular crystallography, practice in diffraction analysis evolved from a universal reliance on isomorphous replacement to the eventual domination of anomalous diffraction for de novo structure determination. As the Protein Data Bank (PDB) grew and familial relationships among proteins became clear, molecular replacement overtook all other phasing methods; however, experimental phasing remained essential for molecules without obvious precedents, with multi- and single-wavelength anomalous diffraction (MAD and SAD) predominating. While the mathematics-based direct methods had proved to be inadequate for typical macromolecules, they returned to crack substantial selenium substructures in SAD analyses of selenomethionyl proteins. Native SAD, exploiting the intrinsic S and P atoms of biomolecules, has become routine. Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. Currently, molecular replacement with AlphaFold models often obviates the need for experimental phase evaluation. For multiple reasons, we are now unfazed by the phase problem. Cryo-EM analysis is an attractive alternative to crystallography for many applications faced by today's structural biologists. It simply finesses the phase problem; however, the principles and procedures of diffraction analysis remain pertinent and are adopted in single-particle cryo-EM studies of biomolecules., (open access.)

A commentary on Wayne Hendrickson's article `Facing the phase problem'., (open access.)

We demonstrate that super-wavelength sandwich plasmonic metasurfaces, with the top metal layer consisting of a periodic arrangement of differently sized rectangle patches, can support anomalous diffraction – one first-order diffraction is boosted greatly in a broad bandwidth while another first-order and zero-order diffractions are suppressed. More importantly, by adding and subtracting the patches in a unit cell and adjusting the geometric parameters, high efficiency and broadband first-order diffraction can be easily tuned from visible to near-, mid- and even far-infrared spectral regions. The metasurfaces can be applied as high-performance light dispersive components in beam splitters, thin-film solar cells and spectrometers. [ABSTRACT FROM AUTHOR]

Kesterite-type compound semiconductors, containing copper and zinc, have photovoltaic properties depending on cation distribution in the crystal structure. Anomalous diffraction allows discrimination of isoelectronic cations, in principle allowing a straightforward determination of site occupation factors from data collected at multiple energies close to the X-ray absorption edges of copper and zinc. However, extremely strong correlation between structural parameters precludes this. We present a recipe based on the direct dependency between refined occupation factors and atomic scattering power, which allows to lift the correlations and to detect issues of individual diffraction patterns or assumptions in the model, thereby allowing for reliable quantitative analysis of the Cu/Zn distribution. [ABSTRACT FROM AUTHOR]

The extrinsic scatterance properties of polycrystalline and single crystal Nd:YAG materials are reported. Materials include undoped, 1%, 1.5%, 2%, 4%, and 6% Nd doped polycrystalline YAG, and undoped and 1% Nd doped single crystal YAG. The motivation of this study is to determine the ideal material type, and doping percentage gain media for use in 0.946~\mu \textm Nd:YAG lasers. In-plane bidirectional scatterance distribution function measurements are collected at multiple wavelengths from 0.405 \mu \textm to 1.55 \mu \textm for all samples. Scatterance data is fit to standard models and a total integrated scatter (TIS) for each sample at various wavelengths is determined. Using the TIS at multiple wavelengths, some conclusions on material quality and suitability are presented. A coated sphere anomalous diffraction (ADA) model is developed and applied to known sources of scatter in polycrystalline and single-crystal Nd:YAG. A Kubelka–Munk wavelength-dependant scatter coefficient model is developed using our ADA model. The model provides an accurate estimate of scatter at 0.946 \mu \textm . A comparison of strengths and weaknesses of single-crystal and polycrystalline materials is presented. This comparison reveals a possible continuing problem with background scatter present in single-crystal YAG. [ABSTRACT FROM AUTHOR]

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy. [ABSTRACT FROM AUTHOR]

We report the structural properties of thin magnetic Permalloy films treated by two different methods: broad beam Ga+ ion implantation at an energy of 30keV as well as annealing at different temperatures under ultrahigh vacuum. Transmission electron microscopy imaging and X-ray diffraction measurements have demonstrated that both ion implantation and annealing (above 300°C) lead to further material crystallization and crystallite growth. Whereas annealing (above 400°C) leads to a strain-free state with an almost constant lattice parameter and to a further enhancement of the initial (111) texture, ion beam implantation boosts the growth of small, arbitrarily oriented crystallites and leads to an linear increase in the lattice parameter, introducing microstrain into the sample. The observed decrease in the saturation magnetization for the implanted samples is mainly attributed to the presence of the non-magnetic Ga atoms incorporated in the Permalloy film itself. The increase in the saturation magnetization for the samples annealed at temperatures above 500°C is explained by an arising dewetting effect since no ordered Ni3Fe phase was detected with anomalous X-ray diffraction. [ABSTRACT FROM AUTHOR]

Beamline 08B1-1 is a recently commissioned bending-magnet beamline at the Canadian Light Source. The beamline is designed for automation and remote access. Together with the undulator-based beamline 08ID-1, they constitute the Canadian Macromolecular Crystallography Facility. This paper describes the design, specifications, hardware and software of beamline 08B1-1. A few scientific results using data obtained at the beamline will be highlighted. [ABSTRACT FROM AUTHOR]

Human farnesyl pyrophosphate synthase (hFPPS) produces farnesyl pyrophosphate, an isoprenoid essential for a variety of cellular processes. The enzyme has been well established as the molecular target of the nitrogen-containing bisphosphonates (N-BPs), which are best known for their antiresorptive effects in bone but are also known for their anticancer properties. Crystal structures of hFPPS in ternary complexes with a novel bisphosphonate, YS0470, and the secondary ligands inorganic phosphate (Pi), inorganic pyrophosphate (PPi) and isopentenyl pyrophosphate (IPP) have recently been reported. Only the co-binding of the bisphosphonate with either PPi or IPP resulted in the full closure of the C-terminal tail of the enzyme, a conformational change that is required for catalysis and that is also responsible for the potent in vivo efficacy of N-BPs. In the present communication, a co-crystal structure of hFPPS in complex with YS0470 and two molecules of Pi is reported. The unusually close proximity between these ligands, which was confirmed by anomalous diffraction data, suggests that they interact with one another, with their anionic charges neutralized in their bound state. The structure also showed the tail of the enzyme to be fully disordered, indicating that simultaneous binding of two Pi molecules with a bisphosphonate cannot induce the tail-closing conformational change in hFPPS. Examination of homologous FPPSs suggested that this ligand-dependent tail closure is only conserved in the mammalian proteins. The prevalence of Pi-bound hFPPS structures in the PDB raises a question regarding the in vivo relevance of Pi binding to the function of the enzyme. [ABSTRACT FROM AUTHOR]

Abstract: Dumbbell shaped aggregates are small particles synthesized in precipitation reactors. Their characterization by optical methods needs the chord length distribution (CLD) of such a shape. We present in this paper the analytical calculation of two CLDs corresponding to two different definitions of CLD. Comparison with Monte-Carlo simulations is presented. Good agreement is found between the exact calculation and simulations. [Copyright &y& Elsevier]

De novo structure determination from single-wavelength anomalous diffraction using native sulfur or phospho-rus in biomolecules (native-SAD) is an appealing method to mitigate the labor-intensive production of heavy-atom derivatives and seleno-methio-nyl substitutions. The native-SAD method is particularly attractive for membrane proteins, which are difficult to produce and often recalcitrant to grow into decent-sized crystals. Native-SAD uses lower-energy X-rays to enhance anomalous signals from sulfur or phospho-rus. However, at lower energies, the scattering and absorption of air contribute to the background noise, reduce the signals and are thus adverse to native-SAD phasing. We have previously demonstrated native-SAD phasing at an energy of 5 keV in air at the NSLS-II FMX beamline. Here, the use of a helium path developed to reduce both the noise from background scattering and the air absorption of the diffracted X-ray beam are described. The helium path was used for collection of anomalous diffraction data at 5 keV for two proteins: thaumatin and the membrane protein TehA. Although anomalous signals from each individual crystal are very weak, robust anomalous signals are obtained from data assembled from micrometre-sized crystals. The thaumatin structure was determined from 15 microcrystals and the TehA structure from 18 microcrystals. These results demonstrate the usefulness of a helium environment in support of native-SAD phasing at 5 keV., (© Akira Karasawa et al. 2022.)