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The transmission of the optical components of the Bernina branch of the Aramis beamline at SwissFEL has been measured with an X-ray gas monitor from DESY and compared with a PSI gas detector upstream of the optical components. The transmission efficiencies of the Mo, Si and SiC mirror coatings of the Aramis beamline and the various other in-beam components were evaluated and compared with theoretical calculations, showing an agreement of 6% or better in all cases. The experiment has also shown the efficacy of the high-harmonic rejection mirrors at the Bernina branch of the Aramis beamline at SwissFEL, and characterized the transmission efficiency of the on-line spectrometer in the Aramis beamline. The theoretical transmission of the mirror coatings match the experimental data to within 7%. The accuracy of these measurements was checked against a radiative bolometer from a Japanese collaboration and found to agree to a level of 4% or better. Further comparisons with a diamond detector from a US-based inter-institute collaboration demonstrated a good agreement for the attenuator settings of the beamline.

A simple and robust tool for spatio-temporal overlap of THz and XUV pulses in in-vacuum pump–probe experiments is presented. The technique exploits ultrafast changes of the optical properties in semiconductors (i.e. silicon) driven by ultrashort XUV pulses that are probed by THz pulses. This work demonstrates that this tool can be used for a large range of XUV fluences that are significantly lower than when probing by visible and near-infrared pulses. This tool is mainly targeted at emerging X-ray free-electron laser facilities, but can be utilized also at table-top high-harmonics sources.

In transmission X-ray microscopy (TXM) systems, the rotation of a scanned sample might be restricted to a limited angular range to avoid collision with other system parts or high attenuation at certain tilting angles. Image reconstruction from such limited angle data suffers from artifacts because of missing data. In this work, deep learning is applied to limited angle reconstruction in TXMs for the first time. With the challenge to obtain sufficient real data for training, training a deep neural network from synthetic data is investigated. In particular, U-Net, the state-of-the-art neural network in biomedical imaging, is trained from synthetic ellipsoid data and multi-category data to reduce artifacts in filtered back-projection (FBP) reconstruction images. The proposed method is evaluated on synthetic data and real scanned chlorella data in 100° limited angle tomography. For synthetic test data, U-Net significantly reduces the root-mean-square error (RMSE) from 2.55 × 10−3 µm−1 in the FBP reconstruction to 1.21 × 10−3 µm−1 in the U-Net reconstruction and also improves the structural similarity (SSIM) index from 0.625 to 0.920. With penalized weighted least-square denoising of measured projections, the RMSE and SSIM are further improved to 1.16 × 10−3 µm−1 and 0.932, respectively. For real test data, the proposed method remarkably improves the 3D visualization of the subcellular structures in the chlorella cell, which indicates its important value for nanoscale imaging in biology, nanoscience and materials science.

X-ray absorption linear dichroism of rutile TiO2 at the Ti K-edge provides information about the electronic states involved in the pre-edge transitions. Here, linear dichroism with high energy resolution is analyzed in combination with ab initio finite difference method calculations and spherical tensor analysis. It provides an assignment of the three pre-edge peaks beyond the octahedral crystal field splitting approximation and estimates the spatial extension of the corresponding final states. It is then discussed for the first time the X-ray absorption (XAS) of pentacoordinated titanium atoms due to oxygen vacancies and it is found that, similarly to anatase TiO2, rutile is expected to exhibit a transition on the low-energy side of peak A3. Its apparent absence in the experiment is related to the degree of p–d orbital mixing which is small in rutile due to its centrosymmetric point group. A recent XAS linear dichroism study on anatase TiO2 single crystals has shown that peak A2 has an intrinsic origin and is due to a quadrupolar transition to the 3d energy levels. In rutile, due to its centrosymmetric point group, the corresponding peak A2 has a small dipole moment explaining the weak transition. The results are confronted with recent picosecond X-ray absorption spectroscopy on rutile TiO2 nanoparticles.

Possibilities in auxiliary technique combinations with small- and wide-angle X ray scattering are described, as well as more complicated sample environments used in X-ray and neutron scattering.

A review of recent and ongoing development and results within the field of biological solution small-angle X-ray scattering (BioSAXS), with a focus on the increasing complexity of biological samples, data collection and data evaluation strategies.

Decision day looms over Ellesmere Port shale gas plan  Cheshire Live

Small earthquake recorded in Stirling on Christmas Day  Daily Record

Lockdown has cut Britain's vibrations, seismologists find  The Guardian

'Sonic boom' as small earthquake shakes Cornwall  ITV News

Explained: How coronavirus lockdown reduced Earth’s seismic noise levels  The Indian Express

European lockdown a boon to seismologists checking Earth's vibrations  E&T Magazine

UK sees notable reduction in seismic noise caused by human activity – experts  Aberdeen Evening Express

The bacterial type VI secretion system (T6SS) secretes many toxic effectors to gain advantage in interbacterial competition and for eukaryotic host infection. The cognate immunity proteins of these effectors protect bacteria from their own effectors. PldB is a T6SS trans-kingdom effector in Pseudomonas aeruginosa that can infect both prokaryotic and eukaryotic cells. Three proteins, PA5086, PA5087 and PA5088, are employed to suppress the toxicity of PldB-family proteins. The structures of PA5087 and PA5088 have previously been reported, but the identification of further distinctions between these immunity proteins is needed. Here, the crystal structure of PA5086 is reported at 1.90 Å resolution. A structural comparison of the three PldB immunity proteins showed vast divergences in their electrostatic potential surfaces. This interesting phenomenon provides an explanation of the stockpiling mechanism of T6SS immunity proteins.

Protein–protein and protein–ligand interactions often involve conformational changes or structural rearrangements that can be quantified by solution small-angle X-ray scattering (SAXS). These scattering intensity measurements reveal structural details of the bound complex, the number of species involved and, additionally, the strength of interactions if carried out as a titration. Although a core part of structural biology workflows, SAXS-based titrations are not commonly used in drug discovery contexts. This is because prior knowledge of expected sample requirements, throughput and prediction accuracy is needed to develop reliable ligand screens. This study presents the use of the histidine-binding protein (26 kDa) and other periplasmic binding proteins to benchmark ligand screen performance. Sample concentrations and exposure times were varied across multiple screening trials at four beamlines to investigate the accuracy and precision of affinity prediction. The volatility ratio between titrated scattering curves and a common apo reference is found to most reliably capture the extent of structural and population changes. This obviates the need to explicitly model scattering intensities of bound complexes, which can be strongly ligand-dependent. Where the dissociation constant is within 102 of the protein concentration and the total exposure times exceed 20 s, the titration protocol presented at 0.5 mg ml−1 yields affinities comparable to isothermal titration calorimetry measurements. Estimated throughput ranges between 20 and 100 ligand titrations per day at current synchrotron beamlines, with the limiting step imposed by sample handling and cleaning procedures.

A novel monoclinic phase of human insulin co-crystallized with m-cresol was structurally characterized by means of powder and single-crystal X-ray diffraction.

The crystal structure of the c-type cytochrome NirC from Pseudomonas aeruginosa has been determined and reveals the simultaneous presence of monomers and 3D domain-swapped dimers in the same asymmetric unit.

Structures of the immunodominant protein P46 from M. hyopneumoniae has been determined by X-ray crystallography and it is shown that P46 can bind a diversity of oligosaccharides, particularly xylose, which exhibits a very high affinity for this protein. Structures of a monoclonal antibody, both alone and in complex with P46, that was raised against M. hyopnemoniae cells and specifically recognizes P46 are also reported.

Rice AKR in the apo structure reveals the ordered open conformation and its key residues which form the substrate channel wall and determine its substrate preference for straight-chain aldehydes.

The title complex, [Os3(C2H4N)H(CO)10] or [Os3(CO)10(μ-H)(μ-HN=C—CH3-1κN:2κC)], was synthesized in 41.6% yield by reactions between Os3(CO)11(CH3CN) and 2,4,6-tri­methyl­hexa­hydro-1,3,5-triazine. The central osmium triangle has two OsI atoms bridged by a hydride ligand and a μ-HN= C—CH3-1κN:2κC triazine fragment. Three CO ligands complete the coordination sphere around each OsI atom, while the remaining Os0 atom has four CO ligands. Each Os atom exhibits a pseudo-octa­hedral coordination environment, discounting the bridging Os—Os bond.

The structure of the title compound, [Os(C6HF4S)4{P(C6H5)3}], has been previously reported [Arroyo et al. (1994). J. Chem. Soc. Dalton Trans. pp. 1819–1824], in the space group Poverline{1}. We have now obtained a monoclinic polymorph for this compound, crystallized from ethanol, while the previous form was obtained from a hexa­ne/chloro­form mixture. The mol­ecular structure is based on a trigonal–bipyramidal OsIV coordination geometry, close to that observed previously in the triclinic form.

Six different rare-earth oxyapatites, including Ca2RE8(SiO4)6O2 (RE = La, Nd, Sm, Eu, or Yb) and NaLa9(SiO4)6O2, were synthesized using solution-based processes followed by cold pressing and sinter­ing. The crystal structures of the synthesized oxyapatites were determined from powder X-ray diffraction (P-XRD) and their chemistries verified with electron probe microanalysis (EPMA). All the oxyapatites were isostructural within the hexa­gonal space group P63/m and showed similar unit-cell parameters. The isolated [SiO4]4− tetra­hedra in each crystal are linked by the cations at the 4f and 6h sites occupied by RE3+ and Ca2+ in Ca2RE8(SiO4)6O2 or La3+ and Na+ in NaLa9(SiO4)6O2. The lattice parameters, cell volumes, and densities of the synthesized oxyapatites fit well to the trendlines calculated from literature values.

The isostructural title compounds, poly[piperazin-1-ium [di-μ-bromido-caesium]], {(C4H11N2)[CsBr2]}n, and poly[piperazin-1-ium [di-μ-bromido-rubidium]], {(C4H11N2)[RbBr2]}n, contain singly-protonated piperazin-1-ium cations and unusual ABr6 (A = Cs or Rb) trigonal prisms. The prisms are linked into a distinctive `curtain wall' arrangement propagating in the (010) plane by face and edge sharing. In each case, a network of N—H⋯N, N—H⋯Br and N—H⋯(Br,Br) hydrogen bonds consolidates the structure.

The syntheses and crystal structures of five 2-benzyl­idene-1-benzosuberone [1-benzosuberone is 6,7,8,9-tetra­hydro-5H-benzo[7]annulen-5-one] derivatives, viz. 2-(4-meth­oxy­benzyl­idene)-1-benzosuberone, C19H18O2, (I), 2-(4-eth­oxy­benzyl­idene)-1-benzosuberone, C20H20O2, (II), 2-(4-benzyl­benzyl­idene)-1-benzosuberone, C25H22O2, (III), 2-(4-chloro­benzyl­idene)-1-benzosuberone, C18H15ClO, (IV) and 2-(4-cyano­benzyl­idene)-1-benzosuberone, C19H15NO, (V), are described. The conformations of the benzosuberone fused six- plus seven-membered ring fragments are very similar in each case, but the dihedral angles between the fused benzene ring and the pendant benzene ring differ somewhat, with values of 23.79 (3) for (I), 24.60 (4) for (II), 33.72 (4) for (III), 29.93 (8) for (IV) and 21.81 (7)° for (V). Key features of the packing include pairwise C—H⋯O hydrogen bonds for (II) and (IV), and pairwise C—H⋯N hydrogen bonds for (V), which generate inversion dimers in each case. The packing for (I) and (III) feature C—H⋯O hydrogen bonds, which lead to [010] and [100] chains, respectively. Weak C—H⋯π inter­actions consolidate the structures and weak aromatic π–π stacking is seen in (II) [centroid–centroid separation = 3.8414 (7) Å] and (III) [3.9475 (7) Å]. A polymorph of (I) crystallized from a different solvent has been reported previously [Dimmock et al. (1999) J. Med. Chem. 42, 1358–1366] in the same space group but with a packing motif based on inversion dimers resembling that seen in (IV) in the present study. The Hirshfeld surfaces and fingerprint plots for (I) and its polymorph are com­pared and structural features of the 2-benzyl­idene-1-benzosuberone family of phases are surveyed.

Two polymorphs of the title compound, C19H16N2O3, were obtained from ethano­lic (polymorph I) and methano­lic solutions (polymorph II), respectively. Both polymorphs crystallize in the monoclinic system with four formula units per cell and a complete mol­ecule in the asymmetric unit. The main difference between the mol­ecules of (I) and (II) is the reversed position of the hy­droxy group of the carb­oxy­lic function. All other conformational features are found to be similar in the two mol­ecules. The different orientation of the OH group results in different hydrogen-bonding schemes in the crystal structures of (I) and (II). Whereas in (I) inter­molecular O—H⋯O hydrogen bonds with the pyridazinone carbonyl O atom as acceptor generate chains with a C(7) motif extending parallel to the b-axis direction, in the crystal of (II) pairs of inversion-related O—H⋯O hydrogen bonds with an R22(8) ring motif between two carb­oxy­lic functions are found. The inter­molecular inter­actions in both crystal structures were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.

Instrumentation for time-resolved small-angle neutron scattering measurements with sub-millisecond time resolution, based on Gähler's TISANE (time-involved small-angle neutron experiments) concept, is in operation at NIST's Center for Neutron Research. This implementation of the technique includes novel electronics for synchronizing the neutron pulses from high-speed counter-rotating choppers with a periodic stimulus applied to a sample. Instrumentation details are described along with measurements demonstrating the utility of the technique for elucidating the reorientation dynamics of anisometric magnetic particles.

Traditionally small-molecule crystallographers have not usually observed or recognized significant radiation damage to their samples during diffraction experiments. However, the increased flux densities provided by third-generation synchrotrons have resulted in increasing numbers of observations of this phenomenon. The diversity of types of small-molecule systems means it is not yet possible to propose a general mechanism for their radiation-induced sample decay, however characterization of the effects will permit attempts to understand and mitigate it. Here, systematic experiments are reported on the effects that sample temperature and beam attenuation have on radiation damage progression, allowing qualitative and quantitative assessment of their impact on crystals of a small-molecule test sample. To allow inter-comparison of different measurements, radiation-damage metrics (diffraction-intensity decline, resolution fall-off, scaling B-factor increase) are plotted against the absorbed dose. For ease-of-dose calculations, the software developed for protein crystallography, RADDOSE-3D, has been modified for use in small-molecule crystallography. It is intended that these initial experiments will assist in establishing protocols for small-molecule crystallographers to optimize the diffraction signal from their samples prior to the onset of the deleterious effects of radiation damage.

As is well known, polymers commonly form lamellar crystals, and these assemble further into lamellar stacks and spherulites during quiescent crystallization. Fifty years ago, Vonk and Kortleve constructed the classical small-angle X-ray scattering theory (SAXS) for a lamellar system, in which it was assumed that the lamellar stack had an infinite lateral size [Vonk & Kortleve (1967), Kolloid Z. Z. Polym. 220, 19–24]. Under this assumption, only crystal planes satisfying the Bragg condition can form strong scattering, and the scattering from the lamellar stack arises from the difference between the scattering intensities in the amorphous and crystalline layers, induced by the incident X-ray beam. This assumption is now deemed unreasonable. In a real polymer spherulite, the lamellar crystal commonly has dimensions of only a few hundred nanometres. At such a limited lateral size, lamellar stacks in a broad orientation have similar scattering, so interference between these lamellar stacks must be considered. Scattering from lamellar stacks parallel to the incident X-ray beam also needs to be considered when total reflection occurs. In this study, various scattering contributions from lamellar stacks in a spherulite are determined. It is found that, for a limited lateral size, the scattering induced by the incident X-ray beam is not the main origin of SAXS. It forms double peaks, which are not observed in real scattering because of destructive interference between the lamellar stacks. The scattering induced by the evanescent wave is the main origin. It can form a similar interference pattern to that observed in a real SAXS measurement: a Guinier region in the small-q range, a signal region in the intermediate-q range and a Porod region in the high-q range. It is estimated that, to avoid destructive interference, the lateral size needs to be greater than 11 µm, which cannot be satisfied in a real lamellar system. Therefore, SAXS in a real polymer system arises largely from the scattering induced by the evanescent wave. Evidence for the existence of the evanescent wave was identified in the scattering of isotactic polypropyl­ene. This study corrects a long-term misunderstanding of SAXS in a polymer lamellar system.