Monitoring coastal change from space  British Geological Survey

The crystal structure of calcium atorvastatin trihydrate was redetermined from previously published synchrotron powder diffraction data to give a much-improved agreement with two independent density-functional theory calculations.

With ever-improving quantum-mechanical computational methods, the accuracy requirements for experimental crystal structures increase. The crystal structure of calcium atorvastatin trihydrate, which has 56 degrees of freedom when determined with a real-space algorithm, was determined from powder diffraction data by Hodge et al. [Powder Diffr. (2020), 35, 136–143]. The crystal structure was a good fit to the experimental data, indicating that the electron density had been captured essentially correctly, but two independent quantum-mechanical calculations disagreed with the experimental structure and with each other. Using the same experimental data, the crystal structure was redetermined from scratch and it was shown that it can be reproduced within a root-mean-square Cartesian displacement of 0.1 Å by two independent quantum-mechanical calculations. The consequences for the calculated energies and solubilities are described.

Hydraulic fracking exposes shale plays to acidic hydraulic fracking fluid (HFF), releasing toxic uranium (U) along with the desired oil and gas. With no existing methods to ensure U remains sequestered in the shale, this study sought to add organic ligands to HFF to explore potential U retention in shale plays. To test this possibility, incubations were set up in which uranyl acetate and one organic bipyridine ligand (either 2,2'-, 2,3'-, 2,4'-, or 4,4'-bipyridine) were added to pristine HFF as the crystallization medium. After several months and complete evaporation of all volatiles, bulk yellow crystalline material was obtained from the incubations, three of which yielded crystals suitable for single-crystal analysis, resulting in two novel structures and a high-quality structure of a previously described compound. The UO2VI acetate complexes bis(acetato-κ2O,O')(2,2'-bipyridine-κ2N,N')dioxidouranium(VI), [U(C2H3O2)2O2(C10H8N2)2] or [2,2'-bipyridine]UVIO2(CH3CO2)2, (I), and bis(acetato-κ2O,O')(2,4'-bipyridine-κN1')dioxidouranium(VI), [U(C2H3O2)2O2(C10H8N2)2] or [2,4'-bipyridine]2UVIO2(CH3CO2)2, (III), contain eight-coordinate UVI in a pseudo-hexagonal bipyramidal coordination geometry and are molecular, packing via weak C—H...O/N interactions, whereas catena-poly[bis(2,3'-bipyridinium) [di-μ-acetato-μ3-hydroxido-μ-hydroxido-di-μ3-oxido-hexaoxidotriuranium(VI)]–2,3'-bipyridine–water (1/1/1)], (C10H9N2)2[U3(C2H3O2)2O8(OH)2]·C10H8N2·H2O or {[2,3'-bipyridinium]2[2,3'-bipyridine][(UVIO2)3(O)2(OH)2(CH3CO2)2·H2O]}n, (II), forms an ionic one-dimensional polymer with seven-coordinate pentagonal bipyramidal UVI centers and hydrogen-bonding interactions within each chain. The formation of these crystals could indicate the potential for bipyridine to bind with U in shale during fracking, which will be explored in a future study via ICP-MS (inductively coupled plasma mass spectrometry) analyses of U concentration in HFF/bipyridine/shale incubations. The variation seen here between the molecular structures may indicate variance in the ability of bipyridine isomers to form complexes with U, which could impact their ability to retain U within shale in the context of fracking.

A novel automated high-throughput screening approach, ClusterFinder, is reported for finding candidate structures for atomic pair distribution function (PDF) structural refinements. Finding starting models for PDF refinements is notoriously difficult when the PDF originates from nanoclusters or small nanoparticles. The reported ClusterFinder algorithm can screen 104 to 105 candidate structures from structural databases such as the Inorganic Crystal Structure Database (ICSD) in minutes, using the crystal structures as templates in which it looks for atomic clusters that result in a PDF similar to the target measured PDF. The algorithm returns a rank-ordered list of clusters for further assessment by the user. The algorithm has performed well for simulated and measured PDFs of metal–oxido clusters such as Keggin clusters. This is therefore a powerful approach to finding structural cluster candidates in a modelling campaign for PDFs of nanoparticles and nanoclusters.

Recent advances in quantum crystallography have shown that, beyond conventional charge density refinement, a one-electron reduced density matrix (1-RDM) satisfying N-representability conditions can be reconstructed using jointly experimental X-ray structure factors and directional Compton profiles (DCP) through semidefinite programming. So far, such reconstruction methods for 1-RDM, not constrained to idempotency, have been tested only on a toy model system (CO2). In this work, a new method is assessed on crystalline urea [CO(NH2)2] using static (0 K) and dynamic (50 K) artificial experimental data. An improved model, including symmetry constraints and frozen core-electron contribution, is introduced to better handle the increasing system complexity. Reconstructed 1-RDMs, deformation densities and DCP anisotropy are analysed, and it is demonstrated that the changes in the model significantly improve the reconstruction quality, even when there is insufficient information and data corruption. The robustness of the model and the strategy are thus shown to be well adapted to address the reconstruction problem from actual experimental scattering data.

Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpWKP) is reported at 3.2 Å resolution. OmpWKP forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpWEC) and OmpWKP show high conservation despite sequence variability in the extracellular loops.

Sorghum, a short-day tropical plant, has been adapted for temperate grain production, in particular through the selection of variants at the MATURITY loci (Ma1–Ma6) that reduce photoperiod sensitivity. Ma3 encodes phytochrome B (phyB), a red/far-red photochromic biliprotein photoreceptor. The multi-domain gene product, comprising 1178 amino acids, autocatalytically binds the phytochromobilin chromophore to form the photoactive holophytochrome (Sb.phyB). This study describes the development of an efficient heterologous overproduction system which allows the production of large quantities of various holoprotein constructs, along with purification and crystallization procedures. Crystals of the Pr (red-light-absorbing) forms of NPGP, PGP and PG (residues 1–655, 114–655 and 114–458, respectively), each C-terminally tagged with His6, were successfully produced. While NPGP crystals did not diffract, those of PGP and PG diffracted to 6 and 2.1 Å resolution, respectively. Moving the tag to the N-terminus and replacing phytochromobilin with phycocyanobilin as the ligand produced PG crystals that diffracted to 1.8 Å resolution. These results demonstrate that the diffraction quality of challenging protein crystals can be improved by removing flexible regions, shifting fusion tags and altering small-molecule ligands.

Mycobacterium tuberculosis can reside and persist in deep tissues; latent tuberculosis can evade immune detection and has a unique mechanism to convert it into active disease through reactivation. M. tuberculosis Rv1421 (MtRv1421) is a hypothetical protein that has been proposed to be involved in nucleotide binding-related metabolism in cell-growth and cell-division processes. However, due to a lack of structural information, the detailed function of MtRv1421 remains unclear. In this study, a truncated N-terminal domain (NTD) of MtRv1421, which contains a Walker A/B-like motif, was purified and crystallized using PEG 400 as a precipitant. The crystal of MtRv1421-NTD diffracted to a resolution of 1.7 Å and was considered to belong to either the C-centered monoclinic space group C2 or the I-centered orthorhombic space group I222, with unit-cell parameters a = 124.01, b = 58.55, c = 84.87 Å, β = 133.12° or a = 58.53, b = 84.86, c = 90.52 Å, respectively. The asymmetric units of the C2 or I222 crystals contained two or one monomers, respectively. In terms of the binding ability of MtRv1421-NTD to various ligands, uridine diphosphate (UDP) and UDP-N-acetylglucosamine significantly increased the melting temperature of MtRv1421-NTD, which indicates structural stabilization through the binding of these ligands. Altogether, the results reveal that a UDP moiety may be required for the interaction of MtRv1421-NTD as a nucleotide-binding protein with its ligand.

Pseudoalteromonas fuliginea sp. PS47 is a recently identified marine bacterium that has extensive enzymatic machinery to metabolize polysaccharides, including a locus that targets pectin-like substrates. This locus contains a gene (locus tag EU509_03255) that encodes a pectin-degrading lyase, called PfPL1, that belongs to polysaccharide lyase family 1 (PL1). The 2.2 Å resolution X-ray crystal structure of PfPL1 reveals the compact parallel β-helix fold of the PL1 family. The back side of the core parallel β-helix opposite to the active site is a meandering set of five α-helices joined by lengthy loops. A comparison of the active site with those of other PL1 enzymes suggests a catalytic mechanism that is independent of metal ions, such as Ca2+, but that substrate recognition may require metal ions. Overall, this work provides the first structural insight into a pectinase of marine origin and the first structure of a PL1 enzyme in subfamily 2.

Crystallographic fragment screening has become a pivotal technique in structure-based drug design, particularly for bacterial targets with a crucial role in infectious disease mechanisms. The enzyme CdaA, which synthesizes an essential second messenger cyclic di-AMP (c-di-AMP) in many pathogenic bacteria, has emerged as a promising candidate for the development of novel antibiotics. To identify crystals suitable for fragment screening, CdaA enzymes from Streptococcus pneumoniae, Bacillus subtilis and Enterococcus faecium were purified and crystallized. Crystals of B. subtilis CdaA, which diffracted to the highest resolution of 1.1 Å, were used to perform the screening of 96 fragments, yielding data sets with resolutions spanning from 1.08 to 1.87 Å. A total of 24 structural hits across eight different sites were identified. Four fragments bind to regions that are highly conserved among pathogenic bacteria, specifically the active site (three fragments) and the dimerization interface (one fragment). The coordinates of the three active-site fragments were used to perform an in silico drug-repurposing screen using the OpenEye suite and the DrugBank database. This screen identified tenofovir, an approved drug, that is predicted to interact with the ATP-binding region of CdaA. Its inhibitory potential against pathogenic E. faecium CdaA has been confirmed by ITC measurements. These findings not only demonstrate the feasibility of this approach for identifying lead compounds for the design of novel antibacterial agents, but also pave the way for further fragment-based lead-optimization efforts targeting CdaA.

Glucose-6-phosphate dehydrogenase (G6PD) is the first enzyme in the pentose phosphate pathway. It has been extensively studied by biochemical and structural techniques. 13 X-ray crystal structures and five electron cryo-microscopy structures in the PDB are focused on in this topical review. Two F420-dependent glucose-6-phosphate dehydrogenase (FGD) structures are also reported. The significant differences between human and parasite G6PDs can be exploited to find selective drugs against infections such as malaria and leishmaniasis. Furthermore, G6PD is a prognostic marker in several cancer types and is also considered to be a tumour target. On the other hand, FGD is considered to be a target against Mycobacterium tuberculosis and possesses a high biotechnological potential in biocatalysis and bioremediation.

Porphyromonas gingivalis is a major pathogenic oral bacterium that is responsible for periodontal disease. It is linked to chronic periodontitis, gingivitis and aggressive periodontitis. P. gingivalis exerts its pathogenic effects through mechanisms such as immune evasion and tissue destruction, primarily by secreting various factors, including cysteine proteases such as gingipain K (Kgp), gingipain R (RgpA and RgpB) and PrtH (UniProtKB ID P46071). Virulence proteins comprise multiple domains, including the pro-peptide region, catalytic domain, K domain, R domain and DUF2436 domain. While there is a growing database of knowledge on virulence proteins and domains, there was no prior evidence or information regarding the structure and biological function of the well conserved DUF2436 domain. In this study, the DUF2436 domain of PrtH from P. gingivalis (PgDUF2436) was determined at 2.21 Å resolution, revealing a noncanonical β-jelly-roll sandwich topology with two antiparallel β-sheets and one short α-helix. Although the structure of PgDUF2436 was determined by the molecular-replacement method using an AlphaFold model structure as a template, there were significant differences in the positions of β1 between the AlphaFold model and the experimentally determined PgDUF2436 structure. The Basic Local Alignment Search Tool sequence-similarity search program showed no sequentially similar proteins in the Protein Data Bank. However, DaliLite search results using structure-based alignment revealed that the PgDUF2436 structure has structural similarity Z-scores of 5.9–5.4 with the C-terminal domain of AlgF, the D4 domain of cytolysin, IglE and the extracellular domain structure of PepT2. This study has elucidated the structure of the DUF2436 domain for the first time and a comparative analysis with similar structures has been performed.

Guanosine 5'-monophosphate (GMP) synthetase (GuaA) catalyzes the last step of GMP synthesis in the purine nucleotide biosynthetic pathway. This enzyme catalyzes a reaction in which xanthine 5'-monophosphate (XMP) is converted to GMP in the presence of Gln and ATP through an adenyl-XMP intermediate. A structure of an XMP-bound form of GuaA from the domain Bacteria has not yet been determined. In this study, the crystal structure of an XMP-bound form of GuaA from the thermophilic bacterium Thermus thermophilus HB8 (TtGuaA) was determined at a resolution of 2.20 Å and that of an apo form of TtGuaA was determined at 2.10 Å resolution. TtGuaA forms a homodimer, and the monomer is composed of three domains, which is a typical structure for GuaA. Disordered regions in the crystal structure were obtained from the AlphaFold2-predicted model structure, and a model with substrates (Gln, XMP and ATP) was constructed for molecular-dynamics (MD) simulations. The structural fluctuations of the TtGuaA dimer as well as the interactions between the active-site residues were analyzed by MD simulations.

Proliferating cell nuclear antigen (PCNA) plays a critical role in DNA replication by enhancing the activity of various proteins involved in replication. In this study, the crystal structure of ApePCNA1, one of three PCNAs from the thermophilic archaeon Aeropyrum pernix, was elucidated. ApePCNA1 was cloned and expressed in Escherichia coli and the protein was purified and crystallized. The resulting crystal structure determined at 2.00 Å resolution revealed that ApePCNA1 does not form a trimeric ring, unlike PCNAs from other domains of life. It has unique structural features, including a long interdomain-connecting loop and a PIP-box-like sequence at the N-terminus, indicating potential interactions with other proteins. These findings provide insights into the functional mechanisms of PCNAs in archaea and their evolutionary conservation across different domains of life. A modified medium and protocol were used to express recombinant protein containing the lac operon. The expression of the target protein increased and the total incubation time decreased when using this system compared with those of previous expression protocols.

A new processing technique for synchrotron scanning 3D X-ray diffraction data is introduced, utilizing symmetric Bragg reflections hkl and hkl, known as Friedel pairs. This technique is designed to tackle the difficulties associated with large, highly deformed, polyphase materials, especially geological samples.

This study examines the quality of charge density obtained by fitting the multipole model to wavefunctions in different basis sets. The complex analysis reveals that changing the basis set quality from double- to triple-zeta can notably improve the charge density related properties of a multipole model.

This study proposes an operation optimization framework for impurity-free recycling of spent lithium-ion batteries. Using a hybrid population balance equation integrated with a data-driven condition classifier, the study firstly identifies the optimal batch and semi-batch operation conditions that significantly reduce the operation time with 100% purity of product; detailed guidelines are given for industrial applications.

The impact of sample thickness and experimental noise on angular correlation analysis from scanning electron nanobeam diffraction patterns of disordered carbon are investigated and analyzed regarding the interpretability of the analysis results.

In the title compound, [Cu2(L)2]·2CH2Cl2, the CuII ions coordinate two (S,O)-chelating aroyl­thio­urea moieties of doubly deprotonated furan-2,5-di­carbonyl­bis­(N,N-di­ethyl­thio­urea) (H2L) ligands. The coordination geometry of the metal centers is best described as a flat isosceles trapezoid with a cis arrangement of the donor atoms.

The present study introduces a processing strategy for synchrotron scanning 3D X-ray diffraction (s3DXRD) data, aimed at addressing the challenges posed by large, highly deformed, polyphase materials such as crystalline rocks. Leveraging symmetric Bragg reflections known as Friedel pairs, our method enables diffraction events to be precisely located within the sample volume. This method allows for fitting the phase, crystal structure and unit-cell parameters at the intra-grain scale on a voxel grid. The processing workflow incorporates several new modules, designed to (i) efficiently match Friedel pairs in large s3DXRD datasets containing up to 108 diffraction peaks; (ii) assign phases to each pixel or voxel, resolving potential ambiguities arising from overlap in scattering angles between different crystallographic phases; and (iii) fit the crystal orientation and unit cell locally on a point-by-point basis. We demonstrate the effectiveness of our technique on fractured granite samples, highlighting the ability of the method to characterize complex geological materials and show their internal structure and mineral composition. Additionally, we include the characterization of a metal gasket made of a commercial aluminium alloy, which surrounded the granite sample during experiments. The results show the effectiveness of the technique in recovering information about the internal texture and residual strain of materials that have undergone high levels of plastic deformation.

This article describes the diffraction pattern (2-periodic Fourier transform) from the vertices of a large patch of the recently discovered `Spectre' tiling – a strictly chiral aperiodic monotile. It was reported recently that the diffraction pattern of the related weakly chiral aperiodic `Hat' monotile was 2-periodic with chiral plane-group symmetry p6 [Kaplan et al. (2024). Acta Cryst. A80, 72–78]. The diffraction periodicity arises because the Hat tiling is a systematic aperiodic deletion of vertices from the 2-periodic hexagonal mta tiling. Despite the similarity of the Hat and Spectre tilings, the Spectre tiling is not aligned with a 2-periodic lattice, and its diffraction pattern is non-periodic with chiral point symmetry 6 about the origin.

Reaction between equimolar amounts of 3,3,3',3'-tetraethyl-1,1'-(furan-2,5-dicarbonyl)bis(thiourea) (H2L) and CuCl2·2H2O in methanol in the presence of the supporting base Et3N gave rise to a neutral dinuclear complex bis[μ-3,3,3',3'-tetraethyl-1,1'-(furan-2,5-dicarbonyl)bis(thioureato)]dicopper(II) dichloromethane disolvate, [Cu2(C16H22N4O3S2)2]·2CH2Cl2 or [Cu2(L)2]·2CH2Cl2. The aroylbis(thioureas) are doubly deprotonated and the resulting anions {L2–} bond to metal ions through (S,O)-chelating moieties. The copper atoms adopt a virtually cis-square-planar environment. In the crystal, adjacent [Cu2(L)2]·2CH2Cl2 units are linked into polymeric chains along the a-axis direction by intermolecular coordinative Cu...S interactions. The co-crystallized solvent molecules play a vital role in the crystal packing. In particular, weak C—Hfuran...Cl and C—Hethyl...Cl contacts consolidate the three-dimensional supramolecular architecture.

X-ray and electron scattering from free gas-phase molecules is examined using the independent atom model (IAM) and ab initio electronic structure calculations. The IAM describes the effect of the molecular geometry on the scattering, but does not account for the redistribution of valence electrons due to, for instance, chemical bonding. By examining the total, i.e. energy-integrated, scattering from three molecules, fluoroform (CHF3), 1,3-cyclohexadiene (C6H8) and naphthalene (C10H8), the effect of electron redistribution is found to predominantly reside at small-to-medium values of the momentum transfer (q ≤ 8 Å−1) in the scattering signal, with a maximum percent difference contribution at 2 ≤ q ≤ 3 Å−1. A procedure to determine the molecular geometry from the large-q scattering is demonstrated, making it possible to more clearly identify the deviation of the scattering from the IAM approximation at small and intermediate q and to provide a measure of the effect of valence electronic structure on the scattering signal.

Coherent X-ray imaging is an active field at synchrotron sources. The images rely on the available coherent flux over a limited field of view. At many synchrotron beamlines a double-crystal monochromator (DCM) is employed in a standard nondispersive arrangement. For coherent diffraction imaging it is advantageous to increase the available field of view by increasing the spatial coherence length (SCL) of a beam exiting such a DCM. Here, Talbot interferometry data together with ray-tracing simulations for a (+ − − +) four-reflection experimental arrangement are presented, wherein the first two reflections are in the DCM and the final fourth reflection is asymmetric at grazing exit. Analyses of the interferometry data combined with the simulations show that compared with the beam exiting the DCM a gain of 76% in the SCL was achieved, albeit with a factor of 20 reduction in flux density, which may not be a severe penalty at a synchrotron beamline. Previous efforts reported in the literature to increase the SCL that employed asymmetric crystal diffraction at grazing incidence are also discussed. A much reduced SCL is found presently in simulations wherein the same asymmetric crystal is set for grazing incidence instead of grazing exit. In addition, the present study is compared and contrasted with two other means of increasing the SCL. These are (i) focusing the beam onto an aperture to act as a secondary source, and (ii) allowing the beam to propagate in vacuum an additional distance along the beamline.

At-wavelength metrology of X-ray optics plays a crucial role in evaluating the performance of optics under actual beamline operating conditions, enabling in situ diagnostics and optimization. Techniques utilizing a wavefront random modulator have gained increasing attention in recent years. However, accurately mapping the measured wavefront slope to a curved X-ray mirror surface when the modulator is downstream of the mirror has posed a challenge. To address this problem, an iterative method has been developed in this study. The results demonstrate a significant improvement compared with conventional approaches and agree with offline measurements obtained from optical metrology. We believe that the proposed method enhances the accuracy of at-wavelength metrology techniques, and empowers them to play a greater role in beamline operation and optics fabrication.

Synchrotron light sources can provide the required spatial coherence, stability and control to support the development of advanced lithography at the extreme ultraviolet and soft X-ray wavelengths that are relevant to current and future fabricating technologies. Here an evaluation of the optical performance of the soft X-ray (SXR) beamline of the Australian Synchrotron (AS) and its suitability for developing interference lithography using radiation in the 91.8 eV (13.5 nm) to 300 eV (4.13 nm) range are presented. A comprehensive physical optics model of the APPLE-II undulator source and SXR beamline was constructed to simulate the properties of the illumination at the proposed location of a photomask, as a function of photon energy, collimation and monochromator parameters. The model is validated using a combination of experimental measurements of the photon intensity distribution of the undulator harmonics. It is shown that the undulator harmonics intensity ratio can be accurately measured using an imaging detector and controlled using beamline optics. Finally, the photomask geometric constraints and achievable performance for the limiting case of fully spatially coherent illumination are evaluated.

Knife-edge imaging is a successful method for determining the wavefront distortion of focusing optics such as Kirkpatrick–Baez mirrors or compound refractive lenses. In this study, the wavefront error of an imperfect elliptical mirror is predicted by developing a knife-edge program using the SHADOW/OASYS platform. It is shown that the focusing optics can be aligned perfectly by minimizing the parabolic and cubic coefficients of the wavefront error. The residual wavefront error provides precise information about the figure/height errors of the focusing optics suggesting it as an accurate method for in situ optical metrology. A Python program is developed to design a customized wavefront refractive corrector to minimize the residual wavefront error. Uniform beam at and out of focus and higher peak intensity are achieved by the wavefront correction in comparison with ideal focusing. The developed code provides a quick way for wavefront error analysis and corrector design for non-ideal optics especially for the new-generation diffraction-limited sources, and saves considerable experimental time and effort.

X-ray ptychography and ptychographic computed tomography have seen a rapid rise since the advent of fourth-generation synchrotrons with a high degree of coherent radiation. In addition to quantitative multiscale structural analysis, ptychography with spectral capabilities has been developed, allowing for spatial-localized multiscale structural and spectral information of samples. The SWING beamline of Synchrotron SOLEIL has recently developed a nanoprobe setup where the endstation's first spectral and resonant ptychographic measurements have been successfully conducted. A metallic nickel wire sample was measured using 2D spectral ptychography in XANES mode and resonant ptychographic tomography. From the 2D spectral ptychography measurements, the spectra of the components of the sample's complex-valued refractive index, δ and β, were extracted, integrated along the sample thickness. By performing resonance ptychographic tomography at two photon energies, 3D maps of the refractive index decrement, δ, were obtained at the Ni K-edge energy and another energy above the edge. These maps allowed the detection of impurities in the Ni wire. The significance of accounting for the atomic scattering factor is demonstrated in the calculation of electron density near a resonance through the use of the δ values. These results indicate that at the SWING beamline it is possible to conduct state-of-the-art spectral and resonant ptychography experiments using the nanoprobe setup.

A reliable `in situ' method for wavefront sensing in the soft X-ray domain is reported, developed for the characterization of rotationally symmetric optical elements, like an ellipsoidal mirror shell. In a laboratory setup, the mirror sample is irradiated by an electron-excited (4.4 keV), micrometre-sized (∼2 µm) fluorescence source (carbon Kα, 277 eV). Substantially, the three-dimensional intensity distribution I(r) is recorded by a CCD camera (2048 × 512 pixels of 13.5 µm) at two positions along the optical axis, symmetrically displaced by ±21–25% from the focus. The transport-of-intensity equation is interpreted in a geometrical sense from plane to plane and implemented as a ray tracing code, to retrieve the phase Φ(r) from the radial intensity gradient on a sub-pixel scale. For reasons of statistical reliability, five intra-/extra-focal CCD image pairs are evaluated and averaged to an annular two-dimensional map of the wavefront error {cal W}. In units of the test wavelength (C Kα), an r.m.s. value sigma_{cal{W}} = ±10.9λ0 and a peak-to-valley amplitude of ±31.3λ0 are obtained. By means of the wavefront, the focus is first reconstructed with a result for its diameter of 38.4 µm, close to the direct experimental observation of 39.4 µm (FWHM). Secondly, figure and slope errors of the ellipsoid are characterized with an average of ±1.14 µm and ±8.8 arcsec (r.m.s.), respectively, the latter in reasonable agreement with the measured focal intensity distribution. The findings enable, amongst others, the precise alignment of axisymmetric X-ray mirrors or the design of a wavefront corrector for high-resolution X-ray science.

The phase problem in the context of focusing synchrotron beams with X-ray lenses is addressed. The feasibility of retrieving the surface error of a lens system by using only the intensity of the propagated beam at several distances is demonstrated. A neural network, trained with a few thousand simulations using random errors, can predict accurately the lens error profile that accounts for all aberrations. It demonstrates the feasibility of routinely measuring the aberrations induced by an X-ray lens, or another optical system, using only a few intensity images.

The simulation of EXAFS spectra of thin films via ab initio methods is discussed. The procedure for producing the spectra is presented as well as an application to a two-dimensional material (WSe2) where the effectiveness of this method in reproducing the spectrum and the linear dichroic response is shown. A series of further examples in which the method has been employed for the structural determination of materials are given.

In situ wavefront sensing plays a critical role in the delivery of high-quality beams for X-ray experiments. X-ray speckle-based techniques stand out among other in situ techniques for their easy experimental setup and various data acquisition modes. Although X-ray speckle-based techniques have been under development for more than a decade, there are still no user-friendly software packages for new researchers to begin with. Here, we present an open-source Python package, spexwavepy, for X-ray wavefront sensing using speckle-based techniques. This Python package covers a variety of X-ray speckle-based techniques, provides plenty of examples with real experimental data and offers detailed online documentation for users. We hope it can help new researchers learn and apply the speckle-based techniques for X-ray wavefront sensing to synchrotron radiation and X-ray free-electron laser beamlines.

MuscleX is an integrated, open-source computer software suite for data reduction of X-ray fiber diffraction patterns from striated muscle and other fibrous systems. It is written in Python and runs on Linux, Microsoft Windows or macOS. Most modules can be run either from a graphical user interface or in a `headless mode' from the command line, suitable for incorporation into beamline control systems. Here, we provide an overview of the general structure of the MuscleX software package and describe the specific features of the individual modules as well as examples of applications.

Achieving diffraction-limited performance in fourth-generation synchrotron radiation sources demands monochromator crystals that can preserve the wavefront across an unprecedented extensive range. There is an urgent need for techniques of absolute crystal diffraction wavefront measurement. At the Beijing Synchrotron Radiation Facility (BSRF), a novel edge scan wavefront metrology technique has been developed. This technique employs a double-edge tracking method, making diffraction-limited level absolute crystal diffraction wavefront measurement a reality. The results demonstrate an equivalent diffraction surface slope error below 70 nrad (corresponding to a wavefront phase error of 4.57% λ) r.m.s. within a nearly 6 mm range for a flat crystal in the crystal surface coordinate. The double-edge structure contributes to exceptional measurement precision for slope error reproducibility, achieving levels below 15 nrad (phase error reproducibility < λ/100) even at a first-generation synchrotron radiation source. Currently, the measurement termed double-edge scan (DES) has already been regarded as a critical feedback mechanism in the fabrication of next-generation crystals.

Advances in physics have been significantly driven by state-of-the-art technology, and in photonics and X-ray science this calls for the ability to manipulate the characteristics of optical beams. Orbital angular momentum (OAM) beams hold substantial promise in various domains such as ultra-high-capacity optical communication, rotating body detection, optical tweezers, laser processing, super-resolution imaging etc. Hence, the advancement of OAM beam-generation technology and the enhancement of its technical proficiency and characterization capabilities are of paramount importance. These endeavours will not only facilitate the use of OAM beams in the aforementioned sectors but also extend the scope of applications in diverse fields related to OAM beams. At the FERMI Free-Electron Laser (Trieste, Italy), OAM beams are generated either by tailoring the emission process on the undulator side or, in most cases, by coupling a spiral zone plate (SZP) in tandem with the refocusing Kirkpatrick–Baez active optic system (KAOS). To provide a robust and reproducible workflow to users, a Hartmann wavefront sensor (WFS) is used for both optics tuning and beam characterization. KAOS is capable of delivering both tightly focused and broad spots, with independent control over vertical and horizontal magnification. This study explores a novel non-conventional `near collimation' operational mode aimed at generating beams with OAM that employs the use of a lithographically manufactured SZP to achieve this goal. The article evaluates the mirror's performance through Hartmann wavefront sensing, offers a discussion of data analysis methodologies, and provides a quantitative analysis of these results with ptychographic reconstructions.

The Circular Electron–Positron Collider (CEPC) in China can also work as an excellent powerful synchrotron light source, which can generate high-quality synchrotron radiation. This synchrotron radiation has potential advantages in the medical field as it has a broad spectrum, with energies ranging from visible light to X-rays used in conventional radiotherapy, up to several megaelectronvolts. FLASH radiotherapy is one of the most advanced radiotherapy modalities. It is a radiotherapy method that uses ultra-high dose rate irradiation to achieve the treatment dose in an instant; the ultra-high dose rate used is generally greater than 40 Gy s−1, and this type of radiotherapy can protect normal tissues well. In this paper, the treatment effect of CEPC synchrotron radiation for FLASH radiotherapy was evaluated by simulation. First, a Geant4 simulation was used to build a synchrotron radiation radiotherapy beamline station, and then the dose rate that the CEPC can produce was calculated. A physicochemical model of radiotherapy response kinetics was then established, and a large number of radiotherapy experimental data were comprehensively used to fit and determine the functional relationship between the treatment effect, dose rate and dose. Finally, the macroscopic treatment effect of FLASH radiotherapy was predicted using CEPC synchrotron radiation through the dose rate and the above-mentioned functional relationship. The results show that the synchrotron radiation beam from the CEPC is one of the best beams for FLASH radiotherapy.

Beauveriolides, including the main beauveriolide I {systematic name: (3R,6S,9S,13S)-9-benzyl-13-[(2S)-hexan-2-yl]-6-methyl-3-(2-methyl­prop­yl)-1-oxa-4,7,10-tri­aza­cyclo­tridecane-2,5,8,11-tetrone, C27H41N3O5}, are a series of cyclo­depsipeptides that have shown promising results in the treatment of Alzheimer's disease and in the prevention of foam cell formation in atherosclerosis. Their crystal structure studies have been difficult due to their tiny crystal size and fibre-like morphology, until now. Recent developments in 3D electron diffraction methodology have made it possible to accurately study the crystal structures of submicron crystals by overcoming the problems of beam sensitivity and dynamical scattering. In this study, the absolute structure of beauveriolide I was determined by 3D electron diffraction. The cyclo­dep­si­peptide crystallizes in the space group I2 with lattice parameters a = 40.2744 (4), b = 5.0976 (5), c = 27.698 (4) Å and β = 105.729 (6)°. After dynamical refinement, its absolute structure was determined by comparing the R factors and calculating the z-scores of the two possible enanti­omorphs of beauveriolide I.

We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small mol­ecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.

The synthesis and structural characterization of three families of coordination com­plexes synthesized from 4'-phenyl-2,2':6',2''-terpyridine (8, Ph-TPY), 4'-(4-chloro­phen­yl)-2,2':6',2''-terpyridine (9, ClPh-TPY) and 4'-(4-meth­oxy­phen­yl)-2,2':6',2''-terpyridine (10, MeOPh-TPY) ligands with the divalent metals Co2+, Fe2+, Mn2+ and Ni2+ are reported. The com­pounds were synthesized from a 1:2 mixture of the metal and ligand, resulting in a series of com­plexes with the general formula [M(R-TPY)2](ClO4)2 (where M = Co2+, Fe2+, Mn2+ and Ni2+, and R-TPY = Ph-TPY, ClPh-TPY and MeOPh-TPY). The general formula and structural and supra­molecular features were determinated by single-crystal X-ray diffraction for bis­(4'-phenyl-2,2':6',2''-terpyridine)­nickel(II) bis­(per­chlo­rate), [Ni(C21H15N3)2](ClO4)2 or [Ni(Ph-TPY)2](ClO4)2, bis­[4'-(4-meth­oxy­phen­yl)-2,2':6',2''-terpyridine]­manganese(II) bis­(per­chlo­rate), [Mn(C22H17N3O)2](ClO4)2 or [Mn(MeOPh-TPY)2](ClO4)2, and bis­(4'-phenyl-2,2':6',2''-ter­py­ridine)­manganese(II) bis­(per­chlo­rate), [Mn(C21H15N3)2](ClO4)2 or [Mn(Ph-TPY)2](ClO4)2. In all three cases, the com­plexes present distorted octa­hedral coordination polyhedra and the crystal packing is determined mainly by weak C—H⋯π inter­actions. All the com­pounds (except for the Ni derivatives, for which FT–IR, UV–Vis and thermal analysis are reported) were fully characterized by spectroscopic (FT–IR, UV–Vis and NMR spectroscopy) and thermal (TGA–DSC, thermogravimetric analysis–differential scanning calorimetry) methods.

The well-known copper car­box­yl­ate dimer, with four car­box­yl­ate ligands ex­ten­ding outwards towards the corners of a square, has been employed to generate a series of crystalline com­pounds. In particular, this work centres on the use of the 4-hy­droxy­benzoate anion (Hhba−) and its deprotonated phe­nol­ate form 4-oxidobenzoate (hba2−) to obtain complexes with the general formula [Cu2(Hhba)4–x(hba)xL2–y]x−, where L is an axial coligand (including solvent mol­ecules), x = 0, 1 or 2, and y = 0 or 1. In some cases, short hy­dro­gen bonds result in complexes which may be represented as [Cu2(Hhba)2(H0.5hba)2L2]−. The main focus of the investigation is on the formation of a variety of extended networks through hy­dro­gen bonding and, in some crystals, coordinate bonds when bridging coligands (L) are employed. Crystals of [Cu2(Hhba)4(di­ox­ane)2]·4(di­ox­ane) consist of the expected Cu dimer with the Hhba− anions forming hy­dro­gen bonds to 1,4-di­ox­ane mol­ecules which block network formation. In the case of crystals of com­position [Et4N][Cu2(Hhba)2(H0.5hba)2(CH3OH)(H2O)]·2(di­ox­ane), Li[Cu2(Hhba)2(H0.5hba)2(H2O)2]·3(di­ox­ane)·4H2O and [Cu2(Hhba)2(H0.5hba)2(H0.5DABCO)2]·3CH3OH (DABCO is 1,4-di­aza­bicyclo­[2.2.2]octa­ne), square-grid hy­dro­gen-bonded networks are generated in which the complex serves as one type of 4-con­necting node, whilst a second 4-con­necting node is a hy­dro­gen-bonding motif assembled from four phenol/phenolate groups. Another two-dimensional (2D) network based upon a related square-grid structure is formed in the case of [Et4N]2[Cu2(Hhba)2(hba)2(di­ox­ane)2][Cu2(Hhba)4(di­ox­ane)(H2O)]·CH3OH. In [Cu2(Hhba)4(H2O)2]·2(Et4NNO3), a square-grid structure is again apparent, but, in this case, a pair of nitrate anions, along with four phenolic groups and a pair of water mol­ecules, combine to form a second type of 4-con­necting node. When 1,8-bis­(di­methyl­amino)­naphthalene (bdn, `proton sponge') is used as a base, another square-grid network is generated, i.e. [Hbdn]2[Cu2(Hhba)2(hba)2(H2O)2]·3(di­ox­ane)·H2O, but with only the copper dimer complex serving as a 4-con­necting node. Complex three-dimensional networks are formed in [Cu2(Hhba)4(O-bipy)]·H2O and [Cu2(Hhba)4(O-bipy)2]·2(di­ox­ane), where the potentially bridging 4,4'-bi­pyridine N,N'-dioxide (O-bipy) ligand is employed. Rare cases of mixed car­box­yl­ate copper dimer complexes were obtained in the cases of [Cu2(Hhba)3(OAc)(di­ox­ane)]·3.5(di­ox­ane) and [Cu2(Hhba)2(OAc)2(DABCO)2]·10(di­ox­ane), with each structure possessing a 2D network structure. The final com­pound re­por­ted is a simple hy­dro­gen-bonded chain of com­position (H0.5DABCO)(H1.5hba), formed from the reaction of H2hba and DABCO.

The activation of C—C bonds by transition-metal com­plexes is of continuing inter­est and aceto­nitrile (MeCN) has attracted attention as a cyanide source with com­paratively low toxicity for organic cyanation reactions. A di­iron end-on μ-η1:η1-CN-bridged com­plex was obtained from a crystallization experiment of an open-chain iron–NHC com­plex, namely, μ-cyanido-κ2C:N-bis­{[(aceto­nitrile-κN)[3,3'-bis­(pyridin-2-yl)-1,1'-(methyl­idene)bis­(benzimidazol-2-yl­idene)]iron(II)} tris­(hexa­fluoro­phos­phate), [Fe2(CN)(C2H3N)2(C25H18N6)2](PF6)3. The cyanide appears to originate from the MeCN solvent by C—C bond cleavage or through carbon–hy­dro­gen oxidation.

Over the last decade, the development of time-resolved serial crystallography (TR-SX) at X-ray free-electron lasers (XFELs) and synchrotrons has allowed researchers to study phenomena occurring in proteins on the femtosecond-to-minute timescale, taking advantage of many technical and methodological breakthroughs. Protein crystals of various sizes are presented to the X-ray beam in either a static or a moving medium. Photoactive proteins were naturally the initial systems to be studied in TR-SX experiments using pump–probe schemes, where the pump is a pulse of visible light. Other reaction initiations through small-molecule diffusion are gaining momentum. Here, selected examples of XFEL and synchrotron time-resolved crystallography studies will be used to highlight the specificities of the various instruments and methods with respect to time resolution, and are compared with cryo-trapping studies.

Mevalonate kinase is central to the isoprenoid biosynthesis pathway. Here, high-resolution X-ray crystal structures of two mevalonate kinases are presented: a eukaryotic protein from Ramazzottius varieornatus and an archaeal protein from Methanococcoides burtonii. Both enzymes possess the highly conserved motifs of the GHMP enzyme superfamily, with notable differences between the two enzymes in the N-terminal part of the structures. Biochemical characterization of the two enzymes revealed major differences in their sensitivity to geranyl pyrophosphate and farnesyl pyrophosphate, and in their thermal stabilities. This work adds to the understanding of the structural basis of enzyme inhibition and thermostability in mevalonate kinases.

A considerable bottleneck in serial crystallography at XFEL and synchrotron sources is the efficient production of large quantities of homogenous, well diffracting microcrystals. Efficient high-throughput screening of batch-grown microcrystals and the determination of ground-state structures from different conditions is thus of considerable value in the early stages of a project. Here, a highly sample-efficient methodology to measure serial crystallography data from microcrystals by raster scanning within standard in situ 96-well crystallization plates is described. Structures were determined from very small quantities of microcrystal suspension and the results were compared with those from other sample-delivery methods. The analysis of a two-dimensional batch crystallization screen using this method is also described as a useful guide for further optimization and the selection of appropriate conditions for scaling up microcrystallization.

The Azotobacter vinelandii FeSII protein forms an oxygen-resistant complex with the nitrogenase MoFe and Fe proteins. FeSII is an adrenodoxin-type ferredoxin that forms a dimer in solution. Previously, the crystal structure was solved [Schlesier et al. (2016), J. Am. Chem. Soc. 138, 239–247] with five copies in the asymmetric unit. One copy is a normal adrenodoxin domain that forms a dimer with its crystallographic symmetry mate. The other four copies are in an `open' conformation with a loop flipped out exposing the 2Fe–2S cluster. The open and closed conformations were interpreted as oxidized and reduced, respectively, and the large conformational change in the open configuration allowed binding to nitrogenase. Here, the structure of FeSII was independently solved in the same crystal form. The positioning of the atoms in the unit cell is similar to the earlier report. However, the interpretation of the structure is different. The `open' conformation is interpreted as the product of a crystallization-induced domain swap. The 2Fe–2S cluster is not exposed to solvent, but in the crystal its interacting helix is replaced by the same helix residues from a crystal symmetry mate. The domain swap is complicated, as it is unusual in being in the middle of the protein rather than at a terminus, and it creates arrangements of molecules that can be interpreted in multiple ways. It is also cautioned that crystal structures should be interpreted in terms of the contents of the entire crystal rather than of one asymmetric unit.

Advances in structural biology have relied heavily on synchrotron cryo-crystallography and cryogenic electron microscopy to elucidate biological processes and for drug discovery. However, disparities between cryogenic and room-temperature (RT) crystal structures pose challenges. Here, Cryo2RT, a high-throughput RT data-collection method from cryo-cooled crystals that leverages the cryo-crystallography workflow, is introduced. Tested on endothiapepsin crystals with four soaked fragments, thaumatin and SARS-CoV-2 3CLpro, Cryo2RT reveals unique ligand-binding poses, offers a comparable throughput to cryo-crystallography and eases the exploration of structural dynamics at various temperatures.

Several proteins from plant pathogenesis-related family 10 (PR10) are highly abundant in the latex of opium poppy and have recently been shown to play diverse and important roles in the biosynthesis of benzylisoquinoline alkaloids (BIAs). The recent determination of the first crystal structures of PR10-10 showed how large conformational changes in a surface loop and adjacent β-strand are coupled to the binding of BIA compounds to the central hydrophobic binding pocket. A more detailed analysis of these conformational changes is now reported to further clarify how ligand binding is coupled to the formation and cleavage of an intermolecular disulfide bond that is only sterically allowed when the BIA binding pocket is empty. To decouple ligand binding from disulfide-bond formation, each of the two highly conserved cysteine residues (Cys59 and Cys155) in PR10-10 was replaced with serine using site-directed mutagenesis. Crystal structures of the Cys59Ser mutant were determined in the presence of papaverine and in the absence of exogenous BIA compounds. A crystal structure of the Cys155Ser mutant was also determined in the absence of exogenous BIA compounds. All three of these crystal structures reveal conformations similar to that of wild-type PR10-10 with bound BIA compounds. In the absence of exogenous BIA compounds, the Cys59Ser and Cys155Ser mutants appear to bind an unidentified ligand or mixture of ligands that was presumably introduced during expression of the proteins in Escherichia coli. The analysis of conformational changes triggered by the binding of BIA compounds suggests a molecular mechanism coupling ligand binding to the disruption of an intermolecular disulfide bond. This mechanism may be involved in the regulation of biosynthetic reactions in plants and possibly other organisms.