A complete method of comprehensive and quantitative evaluation of through-silicon via reliability using a highly sensitive phase-contrast X-ray microtomography was established. Quantitative characterizations include 3D local morphology and overall consistency of statistics.

Phase-contrast enhanced micro-computed tomography reveals huge discontinuities at the interfaces between dental fillings and the tooth substrate. Despite the complex micromorphology, gaps in bonding could be visualized and quantified in 3D.

GIDVis is a software package based on MATLAB specialized for, but not limited to, the visualization and analysis of grazing-incidence thin-film X-ray diffraction data obtained during sample rotation around the surface normal. GIDVis allows the user to perform detector calibration, data stitching, intensity corrections, standard data evaluation (e.g. cuts and integrations along specific reciprocal-space directions), crystal phase analysis etc. To take full advantage of the measured data in the case of sample rotation, pole figures can easily be calculated from the experimental data for any value of the scattering angle covered. As an example, GIDVis is applied to phase analysis and the evaluation of the epitaxial alignment of pentacene­quinone crystallites on a single-crystalline Au(111) surface.

The open-source Python program PDB2INS is designed to prepare a .ins file for refinement with SHELXL [Sheldrick (2015). Acta Cryst. C71, 3–8], taking atom coordinates and other information from a Protein Data Bank (PDB)-format file. If PDB2INS is provided with a four-character PDB code, both the PDB file and the accompanying mmCIF-format reflection data file (if available) are accessed via the internet from the PDB public archive [Read et al. (2011). Structure, 19, 1395–1412] or optionally from the PDB_REDO server [Joosten, Long, Murshudov & Perrakis (2014). IUCrJ, 1, 213–220]. The SHELX-format .ins (refinement instructions and atomic coordinates) and .hkl (reflection data) files can then be generated without further user intervention, appropriate restraints etc. being added automatically. PDB2INS was tested on the 23 974 X-ray structures deposited in the PDB between 2008 and 2018 that included reflection data to 1.7 Å or better resolution in a recognizable format. After creating the two input files for SHELXL without user intervention, ten cycles of conjugate-gradient least-squares refinement were performed. For 96% of these structures PDB2INS and SHELXL completed successfully without error messages.

The examination of anisotropic nanostructures, such as wires, platelets or spikes, inside a transmission electron microscope is normally performed only in plan view. However, intrinsic defects such as growth twin interfaces could occasionally be concealed from direct observation for geometric reasons, leading to superposition. This article presents the shadow-focused ion-beam technique to prepare multiple electron-beam-transparent cross-section specimens of ZnO nanospikes, via a procedure which could be readily extended to other anisotropic structures. In contrast with plan-view data of the same nanospikes, here the viewing direction allows the examination of defects without superposition. By this method, the coexistence of two twin configurations inside the wurtzite-type structure is observed, namely [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 1) and [2 {overline 1} {overline 1} 0]^{ m W}/(0 1 {overline 1} 3), which were not identified during the plan-view observations owing to superposition of the domains. The defect arrangement could be the result of coalescence twinning of crystalline nuclei formed on the partially molten Zn substrate during the flame-transport synthesis. Three-dimensional defect models of the twin interface structures have been derived and are correlated with the plan-view investigations by simulation.

Cryocooling for macromolecular crystallography is usually performed via plunging the crystal into a liquid cryogen or placing the crystal in a cold gas stream. These two approaches are compared here for the case of nitro­gen cooling. The results show that gas stream cooling, which typically cools the crystal more slowly, yields lower mosaicity and, in some cases, a stronger anomalous signal relative to rapid plunge cooling. During plunging, moving the crystal slowly through the cold gas layer above the liquid surface can produce mosaicity similar to gas stream cooling. Annealing plunge cooled crystals by warming and recooling in the gas stream allows the mosaicity and anomalous signal to recover. For tetragonal thermolysin, the observed effects are less pronounced when the cryosolvent has smaller thermal contraction, under which conditions the protein structures from plunge cooled and gas stream cooled crystals are very similar. Finally, this work also demonstrates that the resolution dependence of the reflecting range is correlated with the cooling method, suggesting it may be a useful tool for discerning whether crystals are cooled too rapidly. The results support previous studies suggesting that slower cooling methods are less deleterious to crystal order, as long as ice formation is prevented and dehydration is limited.

DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL [White, Kirian, Martin, Aquila, Nass, Barty & Chapman (2012). J. Appl. Cryst. 45, 335–341], DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.

Serial crystallography, at both synchrotron and X-ray free-electron laser light sources, is becoming increasingly popular. However, the tools in the majority of crystallization laboratories are focused on producing large single crystals by vapour diffusion that fit the cryo-cooled paradigm of modern synchrotron crystallography. This paper presents several case studies and some ideas and strategies on how to perform the conversion from a single crystal grown by vapour diffusion to the many thousands of micro-crystals required for modern serial crystallography grown by batch crystallization. These case studies aim to show (i) how vapour diffusion conditions can be converted into batch by optimizing the length of time crystals take to appear; (ii) how an understanding of the crystallization phase diagram can act as a guide when designing batch crystallization protocols; and (iii) an accessible methodology when attempting to scale batch conditions to larger volumes. These methods are needed to minimize the sample preparation gap between standard rotation crystallography and dedicated serial laboratories, ultimately making serial crystallography more accessible to all crystallographers.

A hitherto unrecognized resolution effect in neutron Larmor diffraction (LD) is reported, resulting from small-angle neutron scattering (SANS) in the sample. Small distortions of the neutron trajectories by SANS give rise to a blurring of the Bragg angles of the order of a few hundredths of a degree, leading to a degradation of the momentum resolution. This effect is negligible for single crystals but may be significant for polycrystalline or powder samples. A procedure is presented to correct the LD data for the parasitic SANS. The latter is accurately determined by the SESANS technique (spin–echo small-angle neutron scattering), which is readily available on Larmor diffractometers. The analysis technique is demonstrated on LD and SESANS data from α-Fe2O3 powder samples. The resulting d-spacing range agrees with experimental data from high-resolution synchrotron radiation powder diffraction on the same sample.

The residual strain distribution has been measured as a function of depth in both top coat and bond coat in as-received and heat-treated air plasma sprayed thermal barrier coating samples. High-energy synchrotron X-ray beams were used in transmission to produce full Debye–Scherrer rings whose non-circular aspect ratio gave the in-plane and out-of-plane strains far more efficiently than the sin2ψ method. The residual strain in the bond coat is found to be tensile and the strain in the β phase of the as-received sample was measured. The residual strains observed in the top coat were generally compressive (increasing towards the interface), with two kinds of nonlinear trend. These was a `jump' feature near the interface, and in some cases there was another `jump' feature near the surface. It is shown how these trend differences can be correlated to cracks in the coating.

Grazing-incidence small-angle X-ray scattering (GISAXS) coupled with computed tomography (CT) has enabled the visualization of the spatial distribution of nanostructures in thin films. 2D GISAXS images are obtained by scanning along the direction perpendicular to the X-ray beam at each rotation angle. Because the intensities at the q positions contain nanostructural information, the reconstructed CT images individually represent the spatial distributions of this information (e.g. size, shape, surface, characteristic length). These images are reconstructed from the intensities acquired at angular intervals over 180°, but the total measurement time is prolonged. This increase in the radiation dosage can cause damage to the sample. One way to reduce the overall measurement time is to perform a scanning GISAXS measurement along the direction perpendicular to the X-ray beam with a limited interval angle. Using filtered back-projection (FBP), CT images are reconstructed from sinograms with limited interval angles from 3 to 48° (FBP-CT images). However, these images are blurred and have a low image quality. In this study, to optimize the CT image quality, total variation (TV) regularization is introduced to minimize sinogram image noise and artifacts. It is proposed that the TV method can be applied to downsampling of sinograms in order to improve the CT images in comparison with the FBP-CT images.

BornAgain is a free and open-source multi-platform software framework for simulating and fitting X-ray and neutron reflectometry, off-specular scattering, and grazing-incidence small-angle scattering (GISAS). This paper concentrates on GISAS. Support for reflectometry and off-specular scattering has been added more recently, is still under intense development and will be described in a later publication. BornAgain supports neutron polarization and magnetic scattering. Users can define sample and instrument models through Python scripting. A large subset of the functionality is also available through a graphical user interface. This paper describes the software in terms of the realized non-functional and functional requirements. The web site https://www.bornagainproject.org/ provides further documentation.

Clays and soils produce strong small-angle X-ray scattering (SAXS) because they contain large numbers of nanoparticles, namely allophane and ferrihydrite. These nanoparticles are amorphous and have approximately spherical shape with a size of around 3–10 nm. The weight ratios of these nanoparticles will affect the properties of the clays and soils. However, the nanoparticles in clays and soils are not generally quantified and are sometimes ignored because there is no standard method to quantify them. This paper describes a method to quantify nanoparticles in clays and soils with SAXS. This is achieved by deriving normalized SAXS intensities from unit weight of the sample, which are not affected by absorption. By integrating the normalized SAXS intensities over the reciprocal space, one obtains a value that is proportional to the weight ratio of the nanoparticles, proportional to the square of the difference of density between the nanoparticles and the liquid surrounding the nanoparticles, and inversely proportional to the density of the nanoparticles. If the density of the nanoparticles is known, the weight ratio of the nanoparticles can be calculated from the SAXS intensities. The density of nanoparticles was estimated from the chemical composition of the sample. Nanoparticles in colloidal silica, silica gels, mixtures of silica gel and α-aluminium oxide, and synthetic clays have been quantified with the integral SAXS method. The results show that the errors of the weight ratios of nanoparticles are around 25% of the weight ratio. It is also shown that some natural clays contain large fractions of nanoparticles; montmorillonite clay from the Mikawa deposit, pyrophillite clay from the Shokozan deposit and kaolinite clay from the Kanpaku deposit contain 25 (7), 10 (2) and 19 (5) wt% nanoparticles, respectively, where errors are shown in parentheses.

Two methods for reconstructing intragranular strain fields are developed for scanning three-dimensional X-ray diffraction (3DXRD). The methods are compared with a third approach where voxels are reconstructed independently of their neighbours [Hayashi, Setoyama & Seno (2017). Mater. Sci. Forum, 905, 157–164]. The 3D strain field of a tin grain, located within a sample of approximately 70 grains, is analysed and compared across reconstruction methods. Implicit assumptions of sub-problem independence, made in the independent voxel reconstruction method, are demonstrated to introduce bias and reduce reconstruction accuracy. It is verified that the two proposed methods remedy these problems by taking the spatial properties of the inverse problem into account. Improvements in reconstruction quality achieved by the two proposed methods are further supported by reconstructions using synthetic diffraction data.

A method of simulating the neutron scattering by a textured polycrystal is presented. It is based on an expansion of the scattering cross sections in terms of the spherical harmonics of the incident and scattering directions, which is derived from the generalized Fourier expansion of the polycrystal orientation distribution function. The method has been implemented in a Monte Carlo code as a component of the McStas software package, and it has been validated by computing some pole figures of a Zircaloy-4 plate and a Zr–2.5Nb pressure tube, and by simulating an ideal transmission experiment. The code can be used to estimate the background generated by components of neutron instruments such as pressure cells, whose walls are made of alloys with significant crystallographic texture. As a first application, the effect of texture on the signal-to-noise ratio was studied in a simple model of a diffraction experiment, in which a sample is placed inside a pressure cell made of a zirconium alloy. With this setting, the results of two simulations were compared: one in which the pressure-cell wall has a uniform distribution of grain orientations, and another in which the pressure cell has the texture of a Zr–2.5Nb pressure tube. The results showed that the effect of the texture of the pressure cell on the noise of a diffractogram is very important. Thus, the signal-to-noise ratio can be controlled by appropriate choice of the texture of the pressure-cell walls.

BEATRIX, is a new tool for performing data analysis of energy-resolved neutron-imaging experiments involving intense fitting procedures of multi-channel spectra. The use of BEATRIX is illustrated for a test specimen, providing spatially resolved 2D maps for residual strains and Bragg edge heights.

An X-ray cross-correlation study of the impact of ligand composition and salt content on the self-assembly of soft-shell nanoparticles is presented, indicating symmetry-selective formation of order.

Because researchers do not understand the formation mechanism of cocrystals, the preparation of cocrystals is mostly done by trial and error. This study focuses on the cocrystal formation mechanism to improve the efficiency of cocrystal preparation.

By using small-angle neutron scattering (SANS) reinforced by scanning electron microscopy, the fine structure of catalysts for polymer electrolyte fuel cells has been investigated. The experimental data resulting from contrast variation with mixed light and heavy water (H2O/D2O) are well described by a core–shell model with fluctuations in concentration between water and Nafion.

The sin2ψ and cosα methods are compared via diffracting-grain identification from electron backscatter diffraction maps. Artificial textures created by the X-ray diffraction measurements are plotted and X-ray elastic constants of the diffracting-grain sets are computed.

This paper reports on the two-scale fractal structure of chromatin organization in the nucleus of the HeLa cell.

The effects of relative humidity on a tetragonal crystal form of hen egg white lysozyme are studied via in situ laboratory X-ray powder diffraction.

Book review

The design and assembly of two 3D-printed holders for high-throughput in meso in situ fixed-target crystallographic data collection are described.

A calculation procedure for X-ray total scattering and the pair distribution function from a crystalline structural model is presented. It allows one to easily and precisely deal with diffraction-angle-dependent parameters such as the atomic form factor and the resolution of the optics.

This study demonstrates a new preparation method for single-crystal X-ray diffraction samples using a focused ion beam. The results of the structure determination and electron density maps with differently prepared samples are discussed, to evaluate this new method.

New developments in the program CrystalCMP are presented, and the program is tested on a large number of crystal structures extracted from the Cambridge Structural Database.

A new approach to variable-temperature measurements is presented, where the sample temperature changes continuously as a function of position.

The sasPDF method, an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime, is presented. The method is applied to characterize the structure of nanoparticle assemblies with different levels of structural order.

The diffraction response of a single crystal to electric field measured by X-ray diffraction by angles close to π. Such schemes allow one to determine with high (~ 10–5–10–6) accuracy the relative changes in the lattice constant.

A detailed theoretical and experimental comparison of dark-field electron holography (DFEH) and high-resolution X-ray diffraction (HRXRD) is performed. Both techniques are being applied to measure elastic strain in an array of transistors and the role of the geometric phase is emphasized.

A detailed study on chiral compound structures found in the Cambridge Structural Database (CSD) is presented. Solvates, salts and co-crystals have intentionally been excluded, in order to focus on the most basic structures of single enantiomers, scalemates and racemates. Similarity between the latter and structures of achiral monomolecular compounds has been established and utilized to arrive at important conclusions about crystallization of chiral compounds. For example, the fundamental phenomenon of conglomerate formation and, in particular, their frequency of occurrence is addressed. In addition, rarely occurring kryptoracemates and scalemic compounds (anomalous racemates) are discussed. Finally, an extended search of enantiomer solid solutions in the CSD is performed to show that there are up to 1800 instances most probably hiding among the deposited crystal structures, while only a couple of dozen have been previously known and studied.

A study on chiral monomolecular compound structures found in the Cambridge Structural Database is presented.

Most articles dealing with R2TSi3 compounds are only interested in one specific composite or in a series of composites with varying T elements while keeping R fixed (or vice versa). The present work gives an overview of the complete range of 2:1:3 silicides, similar those of Hoffmann & Pöttgen (2001) and Pan et al. (2013). In contrast to the work of Hoffmann & Pöttgen (2001), reasons for formation of the different symmetries and superstructures are discussed. Here, crystallographic properties are in[the] focus, whereas physical and magnetic properties are omitted because those are given by Pan et al. (2013). READS LIKE AN ABSTRACT, please re-write and remove references if possible. Should be two sentences max.

The synthesis, characterization and study of structures from a series of bi­phenyls substituted at positions 3, 3', 4 and 4' with groups connected to the bi­phenyl core through oxygen atoms are presented here. The molecular conformation is extensively studied both in the solid as well as in the liquid state, and the effect of different actors (such as packing and chain length) on the torsion angle between aromatic rings is analyzed.

In the title compound, {[Cu(C14H8O4)(C11H10N4O)(H2O)]·1.25H2O}n, the CuII cations are coordinated in a square-pyramidal fashion by trans carboxylate O-atom donors from two diphenate (dip) ligands, trans pyridyl N-atom donors from two bis(4-pyridyl)urea (bpu) ligands, and a ligated water molecule in the apical position. [Cu(H2O)(dip)(bpu)]n coordination polymer layer motifs are oriented parallel to (overline{1}02). These layer motifs display a standard (4,4) rectangular grid topology and stack in an AAA pattern along the a-axis direction to form the full three-dimensional crystal structure of the title compound, mediated by N—H...O and O—H...O hydrogen bonding patterns involving the water molecules of crystallization.

Insights were obtained into the structure of the 4-hydroxy-tetrahydrodipicolinate synthase from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV and the phylogeny of the aminotransferase pathway for the biosynthesis of lysine.

The crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum is reported. It has high structural similarity to other gluconate 5-dehydrogenase proteins, demonstrating that this enzyme is highly conserved.

This article reports conformational polymorphisms of the EF-hand protein MCFD2 which is involved in glycoprotein transport..

The structure of the Pseudomonas aeruginosa T6SS PldB immunity protein PA5086 is reported at 1.9 Å resolution. Comparison of PA5086 with its homologs PA5087 and PA5088 showed great similarities in sequence and structure, but vast divergences in electrostatic potential surfaces.

Endoplasmic reticulum (ER)-associated degradation (ERAD) is a protein quality-control pathway in eukaryotes in which misfolded ER proteins are polyubiquitylated, extracted and ultimately degraded by the proteasome. This process involves ER membrane-embedded ubiquitin E2 and E3 enzymes, as well as a soluble E2 enzyme (Ubc7 in Saccharomyces cerevisiae and UBE2G2 in mammals). E2-binding regions (E2BRs) that recruit these soluble ERAD E2s to the ER have been identified in humans and S. cerevisiae, and structures of E2–E2BR complexes from both species have been determined. In addition to sequence and structural differences between the human and S. cerevisiae E2BRs, the binding of E2BRs also elicits different biochemical outcomes with respect to E2 charging by E1 and E2 discharge. Here, the Schizosaccharomyces pombe E2BR was identified and purified with Ubc7 to resolve a 1.7 Å resolution co-crystal structure of the E2BR in complex with Ubc7. The S. pombe E2BR binds to the back side of the E2 as an α-helix and, while differences exist, it exhibits greater similarity to the human E2BR. Structure-based sequence alignments reveal differences and conserved elements among these species. Structural comparisons and biochemistry reveal that the S. pombe E2BR presents a steric impediment to E1 binding and inhibits E1-mediated charging, respectively.

A putative open reading frame encoding GTP cyclohydrolase I from Listeria monocytogenes was expressed in a recombinant Escherichia coli strain. The recombinant protein was purified and was confirmed to convert GTP to dihydroneopterin triphosphate (Km = 53 µM; vmax = 180 nmol mg−1 min−1). The protein was crystallized from 1.3 M sodium citrate pH 7.3 and the crystal structure was solved at a resolution of 2.4 Å (Rfree = 0.226) by molecular replacement using human GTP cyclohydrolase I as a template. The protein is a D5-symmetric decamer with ten topologically equivalent active sites. Screening a small library of about 9000 compounds afforded several inhibitors with IC50 values in the low-micromolar range. Several inhibitors had significant selectivity with regard to human GTP cyclohydrolase I. Hence, GTP cyclohydrolase I may be a potential target for novel drugs directed at microbial infections, including listeriosis, a rare disease with high mortality.

Archaea are motile by the rotation of the archaellum. The archaellum switches between clockwise and counterclockwise rotation, and movement along a chemical gradient is possible by modulation of the switching frequency. This modulation involves the response regulator CheY and the archaellum adaptor protein CheF. In this study, two new crystal forms and protein structures of CheY are reported. In both crystal forms, CheY is arranged in a domain-swapped conformation. CheF, the protein bridging the chemotaxis signal transduction system and the motility apparatus, was recombinantly expressed, purified and subjected to X-ray data collection.

The membrane protein EsaA is a conserved component of the type VIIb secretion system. Limited proteolysis of purified EsaA from Staphylococcus aureus USA300 identified a stable 48 kDa fragment, which was mapped by fingerprint mass spectrometry to an uncharacterized extracellular segment of EsaA. Analysis by circular dichroism spectroscopy showed that this fragment folds into a single stable domain made of mostly α-helices with a melting point of 34.5°C. Size-exclusion chromatography combined with multi-angle light scattering indicated the formation of a dimer of the purified extracellular domain. Octahedral crystals were grown in 0.2 M ammonium citrate tribasic pH 7.0, 16% PEG 3350 using the hanging-drop vapor-diffusion method. Diffraction data were analyzed to 4.0 Å resolution, showing that the crystals belonged to the enantiomorphic tetragonal space groups P41212 or P43212, with unit-cell parameters a = 197.5, b = 197.5, c = 368.3 Å, α = β = γ = 90°.

Cytisine, a natural product with high affinity for clinically relevant nicotinic acetylcholine receptors (nAChRs), is used as a smoking-cessation agent. The compound displays an excellent clinical profile and hence there is an interest in derivatives that may be further improved or find use in the treatment of other conditions. Here, the binding of a cytisine derivative modified by the addition of a 3-(hydroxypropyl) moiety (ligand 4) to Aplysia californica acetylcholine-binding protein (AcAChBP), a surrogate for nAChR orthosteric binding sites, was investigated. Isothermal titration calorimetry revealed that the favorable binding of cytisine and its derivative to AcAChBP is driven by the enthalpic contribution, which dominates an unfavorable entropic component. Although ligand 4 had a less unfavorable entropic contribution compared with cytisine, the affinity for AcAChBP was significantly diminished owing to the magnitude of the reduction in the enthalpic component. The high-resolution crystal structure of the AcAChBP–4 complex indicated close similarities in the protein–ligand interactions involving the parts of 4 common to cytisine. The point of difference, the 3-(hydroxypropyl) substituent, appears to influence the conformation of the Met133 side chain and helps to form an ordered solvent structure at the edge of the orthosteric binding site.