Structure determination of riboflavin by synchrotron high-resolution powder X-ray diffraction

The crystal structure of the stable form of vitamin B2 or riboflavin (C17H20N4O6) was solved using high-resolution powder X-ray diffraction (PXRD). The high-resolution PXRD pattern of riboflavin was recorded at room temperature at the European Synchrotron Radiation Facility (Grenoble, France). The starting structural model was generated using a Monte Carlo simulated annealing method. The final structure was obtained through Rietveld refinement. The positions of the H atoms belonging to hydroxy groups were estimated from computational energy minimizations. The symmetry is orthorhombic with the space group P212121 and the following lattice parameters: a = 20.01308, b = 15.07337 and c = 5.31565 Å.

Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography

Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)’s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).

Synchrotron 3D μ-Tomography of Porosity during Hot Isostatic Pressing of a Single-Crystal Nickel-Base Superalloy

The evolution of microporosity in single-crystal nickel-base superalloy CMSX-4 during hot isostatic pressing has been investigated by high resolution tomography at the European Synchrotron Radiation Facility in Grenoble. The kinetic dependencies of microporosity annihilation in the superalloy in initially as-cast and homogenized conditions were obtained. It was shown that smaller homogenization pores of about 5-10 μm in size are rapidly annihilate during hot isostatic pressing, while annihilation of larger solidification pores of size up to a few hundred micrometer takes a long time. After commercial hot isostatic pressing at 1288 °C, 103 MPa, 4 h only rare pores smaller than 20 μm remain, which are not critical for fatigue strength.

Small-wedge synchrotron and serial XFEL datasets for Cysteinyl leukotriene GPCRs

Structural studies of challenging targets such as G protein-coupled receptors (GPCRs) have accelerated during the last several years due to the development of new approaches, including small-wedge and serial crystallography. Here, we describe the deposition of seven datasets consisting of X-ray diffraction images acquired from lipidic cubic phase (LCP) grown microcrystals of two human GPCRs, Cysteinyl leukotriene receptors 1 and 2 (CysLT1R and CysLT2R), in complex with various antagonists. Five datasets were collected using small-wedge synchrotron crystallography (SWSX) at the European Synchrotron Radiation Facility with multiple crystals under cryo-conditions. Two datasets were collected using X-ray free electron laser (XFEL) serial femtosecond crystallography (SFX) at the Linac Coherent Light Source, with microcrystals delivered at room temperature into the beam within LCP matrix by a viscous media microextrusion injector. All seven datasets have been deposited in the open-access databases Zenodo and CXIDB. Here, we describe sample preparation and annotate crystallization conditions for each partial and full datasets. We also document full processing pipelines and provide wrapper scripts for SWSX and SFX data processing.A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00759-w

Br diffusion in phonolitic melts: Comparison with fluorine and chlorine diffusion

Bromine diffusion was measured in two natural phonolitic melts: (1) a K2O-rich (~10 wt%) one synthesized from the white pumice phase of the 79 AD eruption of Vesuvius (Italy), and (2) a Na2O-rich (~10 wt%) one corresponding to the most differentiated melt of the 12 000 BC eruption of the Laacher See (Germany). Experiments were performed at 0.5 and 1.0 GPa, 1250 to 1450 °C, at anhydrous and hydrous (2.65 ± 0.35 wt% of dissolved water) conditions. Experiments conducted with the diffusion-couple technique in the piston cylinder were performed with only bromine diffusing and with the simultaneous diffusion of a halogen mixture (F, Cl, Br) to evaluate the interactions between the halogens during diffusion. The diffusion profiles of Br were measured by X-ray fluorescence using synchrotron radiation microprobe (SYXRF), ID18F, at the European Synchrotron Radiation Facility (ESRF, France). Bromine diffusion displays Arrhenian behavior under anhydrous conditions that is similar when it diffuses alone and when it diffuses with F and Cl. The Br diffusion coefficients range between 2 × 10–12 m2/s at 1250 °C and 1.5 × 10–11 m2/s at 1450 °C for the Na-rich melt and between 3 × 10–12 m2/s at 1250 °C and 2.5 × 10–11 m2/s at 1450 °C for the K-rich melt, at 1.0 GPa. Although Br mobility is independent of F and Cl in anhydrous phonolitic melts, its behavior may be dependent on the dominant alkali in the melt, as previously observed for Cl, but not F. For hydrous experiments, although the data are scattered, the Br diffusivity increases slightly with water and the Na/K ratio seems to influence Br diffusivity. Similarly to noble gases, halogen diffusivity at a given temperature in the phonolitic melts appears related to the ionic porosity of the silicate structure. Compared to basaltic melt, Br diffusivities are approximately one order of magnitude lower in the Na-phonolite melt, because of the difference of the pre-exponential factor. Br mobility appears to be decoupled from melt viscosity, considering the results here.

Insulin polymorphism induced by two polyphenols: new crystal forms and advances in macromolecular powder diffraction

This study focuses on the polymorphism of human insulin (HI) upon the binding of the phenolic derivatives p-coumaric acid or trans-resveratrol over a wide pH range. The determination of the structural behaviour of HI via X-ray powder diffraction (XRPD) and single-crystal X-ray diffraction (SCXRD) is reported. Four distinct polymorphs were identified, two of which have not been reported previously. The intermediate phase transitions are discussed. One of the novel monoclinic polymorphs displays the highest molecular packing among insulin polymorphs of the same space group to date; its structure was elucidated by SCXRD. XRPD data collection was performed using a variety of instrumental setups and a systematic comparison of the acquired data is presented. A laboratory diffractometer was used for screening prior to high-resolution XRPD data collection on the ID22 beamline at the European Synchrotron Radiation Facility. Additional measurements for the most representative samples were performed on the X04SA beamline at the Swiss Light Source (SLS) using the MYTHEN II detector, which allowed the detection of minor previously untraceable impurities and dramatically improved the d-spacing resolution even for poorly diffracting samples.

Instrument-model refinement in normalized reciprocal-vector space for X-ray Laue diffraction

A simple yet efficient instrument-model refinement method for X-ray diffraction data is presented and discussed. The method is based on least-squares minimization of differences between respective normalized (i.e. unit length) reciprocal vectors computed for adjacent frames. The approach was primarily designed to work with synchrotron X-ray Laue diffraction data collected for small-molecule single-crystal samples. The method has been shown to work well on both simulated and experimental data. Tests performed on simulated data sets for small-molecule and protein crystals confirmed the validity of the proposed instrument-model refinement approach. Finally, examination of data sets collected at both BioCARS 14-ID-B (Advanced Photon Source) and ID09 (European Synchrotron Radiation Facility) beamlines indicated that the approach is capable of retrieving goniometer parameters (e.g. detector distance or primary X-ray beam centre) reliably, even when their initial estimates are rather inaccurate.