hr Different packing motifs in the crystal structures of three molecular salts containing the 2-amino-5-carboxyanilinium cation: C7H9N2O2+·Cl−, C7H9N2O2+·Br− and C7H9N2O2+·NO3−·H2O By scripts.iucr.org Published On :: 2020-03-13 The syntheses and crystal structures of three molecular salts of protonated 3,4-diaminobenzoic acid, viz. 2-amino-5-carboxyanilinium chloride, C7H9N2O2+·Cl−, (I), 2-amino-5-carboxyanilinium bromide, C7H9N2O2+·Br−, (II), and 2-amino-5-carboxyanilinium nitrate monohydrate, C7H9N2O2+·NO3−·H2O, (III), are described. The cation is protonated at the meta-N atom (with respect to the carboxy group) in each case. In the crystal of (I), carboxylic acid inversion dimers linked by pairwise O—H⋯O hydrogen bonds are seen and each N—H group forms a hydrogen bond to a chloride ion to result in (100) undulating layers of chloride ions bridged by the inversion dimers into a three-dimensional network. The extended structure of (II) features O—H⋯Br, N—H⋯Br and N—H⋯O hydrogen bonds: the last of these generates C(7) chains of cations. Overall, the packing in (II) features undulating (100) sheets of bromide ions alternating with the organic cations. Intermolecular interactions in the crystal of (III) include O—H⋯O, O—H⋯(O,O), N—H⋯O, N—H⋯N and O—H⋯N links. The cations are linked into (001) sheets, and the nitrate ions and water molecules form undulating chains. Taken together, alternating (001) slabs of organic cations plus anions/water molecules result. Hirshfeld surfaces and fingerprint plots were generated to give further insight into the intermolecular interactions in these structures. The crystal used for the data collection of (II) was twinned by rotation about [100] in reciprocal space in a 0.4896 (15):0.5104 (15) ratio. Full Article text
hr Crystal structure and Hirshfeld surface analysis of 3,4-dihydro-2H-anthra[1,2-b][1,4]dioxepine-8,13-dione By scripts.iucr.org Published On :: 2020-03-27 The title compound, C17H12O4, was synthesized from the dye alizarin. The dihedral angle between the mean plane of the anthraquinone ring system (r.m.s. deviation = 0.039 Å) and the dioxepine ring is 16.29 (8)°. In the crystal, the molecules are linked by C—H⋯O hydrogen bonds, forming sheets lying parallel to the ab plane. The sheets are connected through π–π and C=O⋯π interactions to generate a three-dimensional supramolecular network. Hirshfeld surface analysis was used to investigate intermolecular interactions in the solid-state: the most important contributions are from H⋯H (43.0%), H⋯O/O⋯H (27%), H⋯C/C⋯H (13.8%) and C⋯C (12.4%) contacts. Full Article text
hr Crystal structure of trans-dichlorido(1,4,8,11-tetraazacyclotetradecane-κ4N)chromium(III) bis(formamide-κO)(1,4,8,11-tetraazacyclotetradecane-κ4N)chromium(III) bis[tetrach By scripts.iucr.org Published On :: 2020-04-09 The structure of the title compound, [CrCl2(C10H24N4)][Cr(HCONH2)2(C10H24N4)][ZnCl4]2 (C10H24N4 = 1,4,8,11-tetraazacyclotetradecane, cyclam; HCONH2 = formamide, fa), has been determined from synchrotron X-ray data. The asymmetric unit contains two independent halves of the [CrCl2(cyclam)]+ and [Cr(fa)(cyclam)]3+ cations, and one tetrachloridozincate anion. In each complex cation, the CrIII ion is coordinated by the four N atoms of the cyclam ligand in the equatorial plane and two Cl ligands or two O-bonded formamide molecules in a trans axial arrangement, displaying a distorted octahedral geometry with crystallographic inversion symmetry. The Cr—N(cyclam) bond lengths are in the range 2.061 (2) to 2.074 (2) Å, while the Cr—Cl and Cr—O(fa) bond distances are 2.3194 (7) and 1.9953 (19) Å, respectively. The macrocyclic cyclam moieties adopt the centrosymmetric trans-III conformation with six- and five-membered chelate rings in chair and gauche conformations. The crystal structure is stabilized by intermolecular hydrogen bonds involving the NH or CH groups of cyclam and the NH2 group of coordinated formamide as donors, and Cl atoms of the ZnCl42− anion as acceptors. Full Article text
hr Crystal structure and Hirshfeld surface analysis of 2-phenyl-1H-phenanthro[9,10-d]imidazol-3-ium benzoate By scripts.iucr.org Published On :: 2020-04-24 In the title compound, C21H15N2+·C7H5O2−, 2-phenyl-1H-phenanthro[9,10-d]imidazole and benzoic acid form an ion pair complex. The system is consolidated by hydrogen bonds along with π–π interactions and N—H⋯π interactions between the constituent units. For a better understanding of the crystal structure and intermolecular interactions, a Hirshfeld surface analysis was performed. Full Article text
hr Crystal structure and Hirshfeld surface analysis of 4-{[(anthracen-9-yl)methyl]amino}benzoic acid dimethylformamide monosolvate By scripts.iucr.org Published On :: 2020-04-24 The title compound, C22H17NO2·C3H7NO, was synthesized by condensation of an aromatic aldehyde with a secondary amine and subsequent reduction. It was crystallized from a dimethylformamide solution as a monosolvate, C22H17NO2·C3H7NO. The aromatic molecule is non-planar with a dihedral angle between the mean planes of the aniline moiety and the methyl anthracene moiety of 81.36 (8)°. The torsion angle of the Caryl—CH2—NH—Caryl backbone is 175.9 (2)°. The crystal structure exhibits a three-dimensional supramolecular network, resulting from hydrogen-bonding interactions between the carboxylic OH group and the solvent O atom as well as between the amine functionality and the O atom of the carboxylic group and additional C—H⋯π interactions. Hirshfeld surface analysis was performed to quantify the intermolecular interactions. Full Article text
hr The crystal structures of Fe-bearing MgCO3 sp2- and sp3-carbonates at 98 GPa from single-crystal X-ray diffraction using synchrotron radiation By scripts.iucr.org Published On :: 2020-04-21 The crystal structure of MgCO3-II has long been discussed in the literature where DFT-based model calculations predict a pressure-induced transition of the carbon atom from the sp2 to the sp3 type of bonding. We have now determined the crystal structure of iron-bearing MgCO3-II based on single-crystal X-ray diffraction measurements using synchrotron radiation. We laser-heated a synthetic (Mg0.85Fe0.15)CO3 single crystal at 2500 K and 98 GPa and observed the formation of a monoclinic phase with composition (Mg2.53Fe0.47)C3O9 in the space group C2/m that contains tetrahedrally coordinated carbon, where CO44− tetrahedra are linked by corner-sharing oxygen atoms to form three-membered C3O96− ring anions. The crystal structure of (Mg0.85Fe0.15)CO3 (magnesium iron carbonate) at 98 GPa and 300 K is reported here as well. In comparison with previous structure-prediction calculations and powder X-ray diffraction data, our structural data provide reliable information from experiments regarding atomic positions, bond lengths, and bond angles. Full Article text
hr Structures of three ependymin-related proteins suggest their function as a hydrophobic molecule binder By scripts.iucr.org Published On :: 2019-06-20 Ependymin was first discovered as a predominant protein in brain extracellular fluid in fish and was suggested to be involved in functions mostly related to learning and memory. Orthologous proteins to ependymin called ependymin-related proteins (EPDRs) have been found to exist in various tissues from sea urchins to humans, yet their functional role remains to be revealed. In this study, the structures of EPDR1 from frog, mouse and human were determined and analyzed. All of the EPDR1s fold into a dimer using a monomeric subunit that is mostly made up of two stacking antiparallel β-sheets with a curvature on one side, resulting in the formation of a deep hydrophobic pocket. All six of the cysteine residues in the monomeric subunit participate in the formation of three intramolecular disulfide bonds. Other interesting features of EPDR1 include two asparagine residues with glycosylation and a Ca2+-binding site. The EPDR1 fold is very similar to the folds of bacterial VioE and LolA/LolB, which also use a similar hydrophobic pocket for their respective functions as a hydrophobic substrate-binding enzyme and a lipoprotein carrier, respectively. A further fatty-acid binding assay using EPDR1 suggests that it indeed binds to fatty acids, presumably via this pocket. Additional interactome analysis of EPDR1 showed that EPDR1 interacts with insulin-like growth factor 2 receptor and flotillin proteins, which are known to be involved in protein and vesicle translocation. Full Article text
hr 1 kHz fixed-target serial crystallography using a multilayer monochromator and an integrating pixel detector By scripts.iucr.org Published On :: 2019-08-17 Reliable sample delivery and efficient use of limited beam time have remained bottlenecks for serial crystallography (SX). Using a high-intensity polychromatic X-ray beam in combination with a newly developed charge-integrating JUNGFRAU detector, we have applied the method of fixed-target SX to collect data at a rate of 1 kHz at a synchrotron-radiation facility. According to our data analysis for the given experimental conditions, only about 3 000 diffraction patterns are required for a high-quality diffraction dataset. With indexing rates of up to 25%, recording of such a dataset takes less than 30 s. Full Article text
hr Conformational characterization of full-length X-chromosome-linked inhibitor of apoptosis protein (XIAP) through an integrated approach By scripts.iucr.org Published On :: 2019-08-23 The X-chromosome-linked inhibitor of apoptosis protein (XIAP) is a multidomain protein whose main function is to block apoptosis by caspase inhibition. XIAP is also involved in other signalling pathways, including NF-κB activation and copper homeostasis. XIAP is overexpressed in tumours, potentiating cell survival and resistance to chemotherapeutics, and has therefore become an important target for the treatment of malignancy. Despite the fact that the structure of each single domain is known, the conformation of the full-length protein has never been determined. Here, the first structural model of the full-length XIAP dimer, determined by an integrated approach using nuclear magnetic resonance, small-angle X-ray scattering and electron paramagnetic resonance data, is presented. It is shown that XIAP adopts a compact and relatively rigid conformation, implying that the spatial arrangement of its domains must be taken into account when studying the interactions with its physiological partners and in developing effective inhibitors. Full Article text
hr High-throughput structures of protein–ligand complexes at room temperature using serial femtosecond crystallography By scripts.iucr.org Published On :: 2019-10-10 High-throughput X-ray crystal structures of protein–ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein–ligand complexes using SFX. Full Article text
hr Throughput and resolution with a next-generation direct electron detector By scripts.iucr.org Published On :: 2019-10-24 Direct electron detectors (DEDs) have revolutionized cryo-electron microscopy (cryo-EM) by facilitating the correction of beam-induced motion and radiation damage, and also by providing high-resolution image capture. A new-generation DED, the DE64, has been developed by Direct Electron that has good performance in both integrating and counting modes. The camera has been characterized in both modes in terms of image quality, throughput and resolution of cryo-EM reconstructions. The modulation transfer function, noise power spectrum and detective quantum efficiency (DQE) were determined for both modes, as well as the number of images per unit time. Although the DQE for counting mode was superior to that for integrating mode, the data-collection throughput for this mode was more than ten times slower. Since throughput and resolution are related in single-particle cryo-EM, data for apoferritin were collected and reconstructed using integrating mode, integrating mode in conjunction with a Volta phase plate (VPP) and counting mode. Only the counting-mode data resulted in a better than 3 Å resolution reconstruction with similar numbers of particles, and this increased performance could not be compensated for by the increased throughput of integrating mode or by the increased low-frequency contrast of integrating mode with the VPP. These data show that the superior image quality provided by counting mode is more important for high-resolution cryo-EM reconstructions than the superior throughput of integrating mode. Full Article text
hr 3D-MiXD: 3D-printed X-ray-compatible microfluidic devices for rapid, low-consumption serial synchrotron crystallography data collection in flow By scripts.iucr.org Published On :: 2020-01-16 Serial crystallography has enabled the study of complex biological questions through the determination of biomolecular structures at room temperature using low X-ray doses. Furthermore, it has enabled the study of protein dynamics by the capture of atomically resolved and time-resolved molecular movies. However, the study of many biologically relevant targets is still severely hindered by high sample consumption and lengthy data-collection times. By combining serial synchrotron crystallography (SSX) with 3D printing, a new experimental platform has been created that tackles these challenges. An affordable 3D-printed, X-ray-compatible microfluidic device (3D-MiXD) is reported that allows data to be collected from protein microcrystals in a 3D flow with very high hit and indexing rates, while keeping the sample consumption low. The miniaturized 3D-MiXD can be rapidly installed into virtually any synchrotron beamline with only minimal adjustments. This efficient collection scheme in combination with its mixing geometry paves the way for recording molecular movies at synchrotrons by mixing-triggered millisecond time-resolved SSX. Full Article text
hr Structure of the MICU1–MICU2 heterodimer provides insights into the gatekeeping threshold shift By scripts.iucr.org Published On :: 2020-02-27 Mitochondrial calcium uptake proteins 1 and 2 (MICU1 and MICU2) mediate mitochondrial Ca2+ influx via the mitochondrial calcium uniporter (MCU). Its molecular action for Ca2+ uptake is tightly controlled by the MICU1–MICU2 heterodimer, which comprises Ca2+ sensing proteins which act as gatekeepers at low [Ca2+] or facilitators at high [Ca2+]. However, the mechanism underlying the regulation of the Ca2+ gatekeeping threshold for mitochondrial Ca2+ uptake through the MCU by the MICU1–MICU2 heterodimer remains unclear. In this study, we determined the crystal structure of the apo form of the human MICU1–MICU2 heterodimer that functions as the MCU gatekeeper. MICU1 and MICU2 assemble in the face-to-face heterodimer with salt bridges and methionine knobs stabilizing the heterodimer in an apo state. Structural analysis suggests how the heterodimer sets a higher Ca2+ threshold than the MICU1 homodimer. The structure of the heterodimer in the apo state provides a framework for understanding the gatekeeping role of the MICU1–MICU2 heterodimer. Full Article text
hr CM01: a facility for cryo-electron microscopy at the European Synchrotron By scripts.iucr.org Published On :: 2019-05-28 Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, and many national and international centres have since been created in order to exploit this. Here, a new facility for cryo-electron microscopy focused on single-particle reconstruction of biological macromolecules that has been commissioned at the European Synchrotron Radiation Facility (ESRF) is presented. The facility is operated by a consortium of institutes co-located on the European Photon and Neutron Campus and is managed in a similar fashion to a synchrotron X-ray beamline. It has been open to the ESRF structural biology user community since November 2017 and will remain open during the 2019 ESRF–EBS shutdown. Full Article text
hr Extending the scope of coiled-coil crystal structure solution by AMPLE through improved ab initio modelling By scripts.iucr.org Published On :: 2020-02-25 The phase problem remains a major barrier to overcome in protein structure solution by X-ray crystallography. In recent years, new molecular-replacement approaches using ab initio models and ideal secondary-structure components have greatly contributed to the solution of novel structures in the absence of clear homologues in the PDB or experimental phasing information. This has been particularly successful for highly α-helical structures, and especially coiled-coils, in which the relatively rigid α-helices provide very useful molecular-replacement fragments. This has been seen within the program AMPLE, which uses clustered and truncated ensembles of numerous ab initio models in structure solution, and is already accomplished for α-helical and coiled-coil structures. Here, an expansion in the scope of coiled-coil structure solution by AMPLE is reported, which has been achieved through general improvements in the pipeline, the removal of tNCS correction in molecular replacement and two improved methods for ab initio modelling. Of the latter improvements, enforcing the modelling of elongated helices overcame the bias towards globular folds and provided a rapid method (equivalent to the time requirements of the existing modelling procedures in AMPLE) for enhanced solution. Further, the modelling of two-, three- and four-helical oligomeric coiled-coils, and the use of full/partial oligomers in molecular replacement, provided additional success in difficult and lower resolution cases. Together, these approaches have enabled the solution of a number of parallel/antiparallel dimeric, trimeric and tetrameric coiled-coils at resolutions as low as 3.3 Å, and have thus overcome previous limitations in AMPLE and provided a new functionality in coiled-coil structure solution at lower resolutions. These new approaches have been incorporated into a new release of AMPLE in which automated elongated monomer and oligomer modelling may be activated by selecting `coiled-coil' mode. Full Article text
hr The crystal structure of the heme d1 biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states in crystallo By scripts.iucr.org Published On :: 2020-03-25 Monoheme c-type cytochromes are important electron transporters in all domains of life. They possess a common fold hallmarked by three α-helices that surround a covalently attached heme. An intriguing feature of many monoheme c-type cytochromes is their capacity to form oligomers by exchanging at least one of their α-helices, which is often referred to as 3D domain swapping. Here, the crystal structure of NirC, a c-type cytochrome co-encoded with other proteins involved in nitrite reduction by the opportunistic pathogen Pseudomonas aeruginosa, has been determined. The crystals diffracted anisotropically to a maximum resolution of 2.12 Å (spherical resolution of 2.83 Å) and initial phases were obtained by Fe-SAD phasing, revealing the presence of 11 NirC chains in the asymmetric unit. Surprisingly, these protomers arrange into one monomer and two different types of 3D domain-swapped dimers, one of which shows pronounced asymmetry. While the simultaneous observation of monomers and dimers probably reflects the interplay between the high protein concentration required for crystallization and the structural plasticity of monoheme c-type cytochromes, the identification of conserved structural motifs in the monomer together with a comparison with similar proteins may offer new leads to unravel the unknown function of NirC. Full Article text
hr Three differently coloured polymorphs of 3,6-bis(4-chlorophenyl)-2,5-dipropyl-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione By scripts.iucr.org Published On :: 2019-05-23 In this paper, the conformational polymorphism of a chlorinated diketopyrrolopyrrole (DPP) dye having flexible substituents in a non-hydrogen-bonding system is reported. The propyl-substituted DPP derivative (PR3C) has three polymorphic forms, each showing a different colour (red, orange and yellow). All polymorphs could be obtained concomitantly under various crystallization conditions. The results of the crystal structure analysis indicate that PR3C adopts different conformations in each polymorph. The packing effect caused by the difference in the arrangement of neighbouring molecules was found to play an important role in the occurrence of the observed polymorphism. The thermodynamic stability relationship between the three polymorphs was identified by thermal analysis and indicates that the yellow polymorph is the thermally stable form. The results indicate that the yellow form and orange form are enantiotropically related, and the other polymorph is monotropically related to the others. Full Article text
hr XTIP – the world's first beamline dedicated to the synchrotron X-ray scanning tunneling microscopy technique By scripts.iucr.org Published On :: 2020-04-14 In recent years, there have been numerous efforts worldwide to develop the synchrotron X-ray scanning tunneling microscopy (SX-STM) technique. Here, the inauguration of XTIP, the world's first beamline fully dedicated to SX-STM, is reported. The XTIP beamline is located at Sector 4 of the Advanced Photon Source at Argonne National Laboratory. It features an insertion device that can provide left- or right-circular as well as horizontal- and vertical-linear polarization. XTIP delivers monochromatic soft X-rays of between 400 and 1900 eV focused into an environmental enclosure that houses the endstation instrument. This article discusses the beamline system design and its performance. Full Article text
hr Synchrotron multimodal imaging in a whole cell reveals lipid droplet core organization By scripts.iucr.org Published On :: 2020-04-23 A lipid droplet (LD) core of a cell consists mainly of neutral lipids, triacylglycerols and/or steryl esters (SEs). The structuration of these lipids inside the core is still under debate. Lipid segregation inside LDs has been observed but is sometimes suggested to be an artefact of LD isolation and chemical fixation. LD imaging in their native state and in unaltered cellular environments appears essential to overcome these possible technical pitfalls. Here, imaging techniques for ultrastructural study of native LDs in cellulo are provided and it is shown that LDs are organized structures. Cryo soft X-ray tomography and deep-ultraviolet (DUV) transmittance imaging are showing a partitioning of SEs at the periphery of the LD core. Furthermore, DUV transmittance and tryptophan/tyrosine auto-fluorescence imaging on living cells are combined to obtain complementary information on cell chemical contents. This multimodal approach paves the way for a new label-free organelle imaging technique in living cells. Full Article text
hr Radiochromic film dosimetry in synchrotron radiation breast computed tomography: a phantom study By scripts.iucr.org Published On :: 2020-04-22 This study relates to the INFN project SYRMA-3D for in vivo phase-contrast breast computed tomography using the SYRMEP synchrotron radiation beamline at the ELETTRA facility in Trieste, Italy. This peculiar imaging technique uses a novel dosimetric approach with respect to the standard clinical procedure. In this study, optimization of the acquisition procedure was evaluated in terms of dose delivered to the breast. An offline dose monitoring method was also investigated using radiochromic film dosimetry. Various irradiation geometries have been investigated for scanning the prone patient's pendant breast, simulated by a 14 cm-diameter polymethylmethacrylate cylindrical phantom containing pieces of calibrated radiochromic film type XR-QA2. Films were inserted mid-plane in the phantom, as well as wrapped around its external surface, and irradiated at 38 keV, with an air kerma value that would produce an estimated mean glandular dose of 5 mGy for a 14 cm-diameter 50% glandular breast. Axial scans were performed over a full rotation or over 180°. The results point out that a scheme adopting a stepped rotation irradiation represents the best geometry to optimize the dose distribution to the breast. The feasibility of using a piece of calibrated radiochromic film wrapped around a suitable holder around the breast to monitor the scan dose offline is demonstrated. Full Article text
hr Quantitative three-dimensional nondestructive imaging of whole anaerobic ammonium-oxidizing bacteria By scripts.iucr.org Published On :: 2020-04-17 Anaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and in nitrogenous wastewater treatment. The anammox bacteria ultrastructure is unique and distinctly different from that of other prokaryotic cells. The morphological structure of an organism is related to its function; however, research on the ultrastructure of intact anammox bacteria is lacking. In this study, in situ three-dimensional nondestructive ultrastructure imaging of a whole anammox cell was performed using synchrotron soft X-ray tomography (SXT) and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the intact anammox bacteria were performed. High soft X-ray absorption composition inside anammoxosome was detected and verified to be relevant to iron-binding protein. On this basis, the shape adaptation of the anammox bacteria response to iron was explored. Full Article text
hr High-dynamic-range transmission-mode detection of synchrotron radiation using X-ray excited optical luminescence in diamond By scripts.iucr.org Published On :: 2020-03-13 Enhancement of X-ray excited optical luminescence in a 100 µm-thick diamond plate by introduction of defect states via electron beam irradiation and subsequent high-temperature annealing is demonstrated. The resulting X-ray transmission-mode scintillator features a linear response to incident photon flux in the range 7.6 × 108 to 1.26 × 1012 photons s−1 mm−2 for hard X-rays (15.9 keV) using exposure times from 0.01 to 5 s. These characteristics enable a real-time transmission-mode imaging of X-ray photon flux density without disruption of X-ray instrument operation. Full Article text
hr Zeeman quantum beats of helium Rydberg states excited by synchrotron radiation By scripts.iucr.org Published On :: 2020-03-31 Quantum beats in fluorescence decay from Zeeman-split magnetic sublevels have been measured for helium Rydberg states excited by synchrotron radiation. The Zeeman quantum beats observed in this prototypical case were fitted with an equation from a theoretical formulation. It is proposed that Zeeman quantum beat measurement can be a useful way to simply evaluate the polarization characteristics of extreme ultraviolet light. Full Article text
hr Synchrotron X-ray diffraction investigation of the surface condition of artefacts from King Henry VIII's warship the Mary Rose By scripts.iucr.org Published On :: 2020-04-15 Synchrotron X-ray diffraction (XRD) measured on the XMaS beamline at the ESRF was used to characterize the alloy composition and crystalline surface corrosion of three copper alloy Tudor artefacts recovered from the undersea wreck of King Henry VIII's warship the Mary Rose. The XRD method adopted has a dynamic range ∼1:105 and allows reflections <0.002% of the height of major reflections in the pattern to be discerned above the background without smoothing. Laboratory XRD, scanning electron microscopy–energy dispersive spectroscopy, synchrotron X-ray fluorescence and X-ray excited optical luminescence–X-ray near-edge absorption structure were used as supporting techniques, and the combination revealed structural and compositional features of importance to both archaeology and conservation. The artefacts were brass links believed to be fragments of chainmail and were excavated from the seabed during 1981 and 1982. Their condition reflects very different treatment just after recovery, viz. complete cleaning and conservation, chemical corrosion inhibition and chloride removal only, and distilled water soaking only (to remove the chlorides). The brass composition has been determined for all three at least in the top 7 µm or so as Cu(73%)Zn(27%) from the lattice constant. Measurement of the peak widths showed significant differences in the crystallite size and microstrain between the three samples. All of the links are found to be almost chloride-free with the main corrosion products being spertiniite, sphalerite, zincite, covellite and chalcocite. The balance of corrosion products between the links reflects the conservation treatment applied to one and points to different corrosion environments for the other two. Full Article text
hr Estimating signal and noise of time-resolved X-ray solution scattering data at synchrotrons and XFELs By scripts.iucr.org Published On :: 2020-03-31 Elucidating the structural dynamics of small molecules and proteins in the liquid solution phase is essential to ensure a fundamental understanding of their reaction mechanisms. In this regard, time-resolved X-ray solution scattering (TRXSS), also known as time-resolved X-ray liquidography (TRXL), has been established as a powerful technique for obtaining the structural information of reaction intermediates and products in the liquid solution phase and is expected to be applied to a wider range of molecules in the future. A TRXL experiment is generally performed at the beamline of a synchrotron or an X-ray free-electron laser (XFEL) to provide intense and short X-ray pulses. Considering the limited opportunities to use these facilities, it is necessary to verify the plausibility of a target experiment prior to the actual experiment. For this purpose, a program has been developed, referred to as S-cube, which is short for a Solution Scattering Simulator. This code allows the routine estimation of the shape and signal-to-noise ratio (SNR) of TRXL data from known experimental parameters. Specifically, S-cube calculates the difference scattering curve and the associated quantum noise on the basis of the molecular structure of the target reactant and product, the target solvent, the energy of the pump laser pulse and the specifications of the beamline to be used. Employing a simplified form for the pair-distribution function required to calculate the solute–solvent cross term greatly increases the calculation speed as compared with a typical TRXL data analysis. Demonstrative applications of S-cube are presented, including the estimation of the expected TRXL data and SNR level for the future LCLS-II HE beamlines. Full Article text
hr Fast continuous measurement of synchrotron powder diffraction synchronized with controlling gas and vapour pressures at beamline BL02B2 of SPring-8 By scripts.iucr.org Published On :: 2020-03-16 A gas- and vapour-pressure control system synchronized with the continuous data acquisition of millisecond high-resolution powder diffraction measurements was developed to study structural change processes in gas storage and reaction materials such as metal organic framework compounds, zeolite and layered double hydroxide. The apparatus, which can be set up on beamline BL02B2 at SPring-8, mainly comprises a pressure control system of gases and vapour, a gas cell for a capillary sample, and six one-dimensional solid-state (MYTHEN) detectors. The pressure control system can be remotely controlled via developed software connected to a diffraction measurement system and can be operated in the closed gas and vapour line system. By using the temperature-control system on the sample, high-resolution powder diffraction data can be obtained under gas and vapour pressures ranging from 1 Pa to 130 kPa in temperatures ranging from 30 to 1473 K. This system enables one to perform automatic and high-throughput in situ X-ray powder diffraction experiments even at extremely low pressures. Furthermore, this developed system is useful for studying crystal structures during the adsorption/desorption processes, as acquired by millisecond and continuous powder diffraction measurements. The acquisition of diffraction data can be synchronized with the control of the pressure with a high frame rate of up to 100 Hz. In situ and time-resolved powder diffraction measurements are demonstrated for nanoporous Cu coordination polymer in various gas and vapour atmospheres. Full Article text
hr Forthcoming article in Journal of Synchrotron Radiation By journals.iucr.org Published On :: Full Article Still image
hr Application of a high-throughput microcrystal delivery system to serial femtosecond crystallography By scripts.iucr.org Published On :: 2020-03-25 Microcrystal delivery methods are pivotal in the use of serial femtosecond crystallography (SFX) to resolve the macromolecular structures of proteins. Here, the development of a novel technique and instruments for efficiently delivering microcrystals for SFX are presented. The new method, which relies on a one-dimensional fixed-target system that includes a microcrystal container, consumes an extremely low amount of sample compared with conventional two-dimensional fixed-target techniques at ambient temperature. This novel system can deliver soluble microcrystals without highly viscous carrier media and, moreover, can be used as a microcrystal growth device for SFX. Diffraction data collection utilizing this advanced technique along with a real-time visual servo scan system has been successfully demonstrated for the structure determination of proteinase K microcrystals at 1.85 Å resolution. Full Article text
hr Significant texture improvement in single-crystalline-like materials on low-cost flexible metal foils through growth of silver thin films By journals.iucr.org Published On :: Single-crystalline-like thin films composed of crystallographically aligned grains are a new prototype of 2D materials developed recently for low-cost and high-performance flexible electronics as well as second-generation high-temperature superconductors. In this work, significant texture improvement in single-crystalline-like materials is achieved through growth of a 330 nm-thick silver layer. Full Article text
hr Disorder in La1−xBa1+xGaO4−x/2 ionic conductor: resolving the pair distribution function through insight from first-principles modeling By journals.iucr.org Published On :: Ba excess in LaBaGaO4 triggers ionic conductivity together with structural disorder. A direct correlation is found between the density functional theory model energy and the pair distribution function fit residual. Full Article text
hr Small-angle neutron scattering (SANS) and spin-echo SANS measurements reveal the logarithmic fractal structure of the large-scale chromatin organization in HeLa nuclei By journals.iucr.org Published On :: This paper reports on the two-scale fractal structure of chromatin organization in the nucleus of the HeLa cell. Full Article text
hr Measurement of single crystal piezo modulus by the method of diffraction of synchrotron radiation at angles near π By journals.iucr.org Published On :: 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. Full Article text
hr Pattern matching indexing of Laue and monochromatic serial crystallography data for applications in Materials Science By journals.iucr.org Published On :: An algorithm, based on the matching of q-vectors pairs, is combined with three-dimensional pattern matching using a nearest-neighbors approach to index Laue and monochromatic serial crystallography data recorded on small unit cell samples. Full Article text
hr Synthesis, crystal structure, polymorphism and microscopic luminescence properties of anthracene derivative compounds By journals.iucr.org Published On :: Crystal structure and microscopic optical properties of anthracene derivative compounds have been investigated by single-crystal synchrotron X-ray diffraction, laser confocal microscopy and fluorescence lifetime imaging microscopy. Full Article text
hr STS or Sociology and anthropology with a focus on criminal justice? By www.bleepingcomputer.com Published On :: 2019-12-09T21:55:07-05:00 Full Article
hr Ancient star discovered through patience and clever use of technology By insider.si.edu Published On :: Fri, 05 Mar 2010 19:41:02 +0000 Finding this stellar relic wasn’t easy. It is 60,000 times dimmer than the faintest star visible to the unaided eye. The team also had to distinguish it from many surrounding stars that aren’t so old. Just like an archaeological dig, the hunt succeeded through a combination of patience and clever use of technology. The post Ancient star discovered through patience and clever use of technology appeared first on Smithsonian Insider. Full Article Research News Science & Nature Space astronomy astrophysics bees Smithsonian Astrophysical Observatory technology
hr “Death Star” Shreds, Swallows Dwarf Planet By insider.si.edu Published On :: Tue, 22 Jun 2010 11:23:55 +0000 It seems the stuff of science fiction, but astronomers have found a real-life “Death Star” that shredded a rocky planet and is swallowing the dusty remains. The post “Death Star” Shreds, Swallows Dwarf Planet appeared first on Smithsonian Insider. Full Article Research News Science & Nature Space astronomy astrophysics planets Smithsonian Astrophysical Observatory
hr Smithsonian Scientist Discovers the Moon is Shrinking By insider.si.edu Published On :: Fri, 20 Aug 2010 17:50:24 +0000 Smithsonian scientist Tom Watters explores the universe. His most recent discovery the moon is shrinking. Watch the video to learn more about his research. The post Smithsonian Scientist Discovers the Moon is Shrinking appeared first on Smithsonian Insider. Full Article Research News Science & Nature Space astrophysics National Air and Space Museum
hr Scientists issue call to action for archaeological sites threatened by rising seas, urban development By insider.si.edu Published On :: Fri, 22 Oct 2010 08:41:25 +0000 Should global warming cause sea levels to rise as predicted in coming decades, thousands of archaeological sites in coastal areas around the world will be lost to erosion. With no hope of saving all of these sites, three archaeologists—Leslie Reeder of Southern Methodist University, Jon Erlandson of the University of Oregon and Torben Rick from the Smithsonian's National Museum of Natural History—have issued a call to action for scientists to assess the sites most at risk around the world. The post Scientists issue call to action for archaeological sites threatened by rising seas, urban development appeared first on Smithsonian Insider. Full Article Anthropology Marine Science Research News Science & Nature archaeology climate change National Museum of Natural History
hr White-naped crane chicks thriving at National Zoo By insider.si.edu Published On :: Wed, 15 Dec 2010 12:51:33 +0000 At the Smithsonian Conservation Biology Institute in Front Royal, Va., the seven-month-old white-naped cranes Cal and Bill are thriving. The post White-naped crane chicks thriving at National Zoo appeared first on Smithsonian Insider. Full Article Animals Research News Science & Nature biodiversity captive breeding conservation endangered species Migratory Bird Center Smithsonian's National Zoo veterinary medicine
hr Invasive oriental shrimp found in Chesapeake Bay by Smithsonian scientists By insider.si.edu Published On :: Fri, 07 Jan 2011 18:07:50 +0000 Twenty years ago scientists at the Marine Invasions Lab of the Smithsonian Environmental Research Center in Edgewater, Md., began studying the interactions between native grass […] The post Invasive oriental shrimp found in Chesapeake Bay by Smithsonian scientists appeared first on Smithsonian Insider. Full Article Animals Marine Science Research News Science & Nature biodiversity Chesapeake Bay conservation biology invasive species Smithsonian Environmental Research Center
hr Snowflake Study through Photomicrography, 1890 By insider.si.edu Published On :: Tue, 18 Jan 2011 19:53:36 +0000 Snowflake Study through Photomicrography, 1890 Wilson A. Bentley became fascinated with the crystalline structure of individual snowflakes on his parent’s Vermont farm. By adapting a […] The post Snowflake Study through Photomicrography, 1890 appeared first on Smithsonian Insider. Full Article Science & Nature Snapshot photography Smithsonian Institution Archives
hr New interactive World Wide Telescope tour chronicles career of Harvard-Smithsonian astronomer John Huchra By insider.si.edu Published On :: Fri, 28 Jan 2011 12:43:50 +0000 To honor Harvard-Smithsonian astronomer John Huchra, who passed away in October 2010, his friends and colleagues at the Harvard-Smithsonian Center for Astrophysics have created a […] The post New interactive World Wide Telescope tour chronicles career of Harvard-Smithsonian astronomer John Huchra appeared first on Smithsonian Insider. Full Article Research News Science & Nature Space astrophysics Center for Astrophysics | Harvard & Smithsonian
hr Center for Astrophysics project gets first look through new ALMA telescope By insider.si.edu Published On :: Wed, 05 Oct 2011 17:39:35 +0000 Humanity's most complex ground-based astronomy observatory, the Atacama Large Millimeter/submillimeter Array (ALMA), has officially opened for astronomers at its 16,500-foot high desert plateau in northern Chile. The post Center for Astrophysics project gets first look through new ALMA telescope appeared first on Smithsonian Insider. Full Article Science & Nature Space astronomy astrophysics Center for Astrophysics | Harvard & Smithsonian Smithsonian Astrophysical Observatory
hr Smithsonian Anthropologist Bruce Smith talks turkey…squash, potatoes and corn By insider.si.edu Published On :: Tue, 15 Nov 2011 16:46:21 +0000 Smithsonian Anthropologist Bruce Smith shares the origins of some favorite Thanksgiving foods. The post Smithsonian Anthropologist Bruce Smith talks turkey…squash, potatoes and corn appeared first on Smithsonian Insider. Full Article Research News Science & Nature Peru South America
hr Strange deep sea creatures confirmed as three new species By insider.si.edu Published On :: Tue, 15 Nov 2011 20:19:25 +0000 DNA analysis has established that creatures captured during a voyage to the mid-Atlantic are members of the Torquaratoridae; a recently discovered family of acorn worms. The post Strange deep sea creatures confirmed as three new species appeared first on Smithsonian Insider. Full Article Animals Marine Science Science & Nature biodiversity National Museum of Natural History new species
hr Caribbean box jellyfish now thriving in southern Florida By insider.si.edu Published On :: Thu, 02 Feb 2012 14:28:41 +0000 A box jellyfish from the Caribbean appears to have recently become established in the red mangroves of Florida near Boca Raton. The post Caribbean box jellyfish now thriving in southern Florida appeared first on Smithsonian Insider. Full Article Animals Marine Science Science & Nature Caribbean National Museum of Natural History
hr Black hole came from a shredded galaxy By insider.si.edu Published On :: Wed, 15 Feb 2012 14:11:27 +0000 Astronomers using NASA's Hubble Space Telescope have found a cluster of young, blue stars encircling the first intermediate-mass black hole ever discovered. The presence of the star cluster suggests that the black hole was once at the core of a now-disintegrated dwarf galaxy. The post Black hole came from a shredded galaxy appeared first on Smithsonian Insider. Full Article Science & Nature Space astronomy astrophysics black holes Center for Astrophysics | Harvard & Smithsonian galaxies Smithsonian Astrophysical Observatory
hr Waterworld enshrouded by a thick, steamy atmosphere is new class of planet By insider.si.edu Published On :: Tue, 21 Feb 2012 14:46:48 +0000 Observations by the NASA/ESA Hubble Space Telescope have come up with a new class of planet, a waterworld enshrouded by a thick, steamy atmosphere. It’s smaller than Uranus but larger than Earth. The post Waterworld enshrouded by a thick, steamy atmosphere is new class of planet appeared first on Smithsonian Insider. Full Article Science & Nature Space astronomy astrophysics Center for Astrophysics | Harvard & Smithsonian planets Smithsonian Astrophysical Observatory