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82 results for “x-ray structure”
Chemical and Structural In-Situ Characterization of Model Electrocatalysts by Combined Infrared Spectroscopy and Surface X-Ray Diffraction
<p>Raw and treated data</p>
Exploring the chemical and structural change of copper porphyrins upon charging by means of synchrotron X-ray absorption spectroscopy
<h2><span>Abstract</span></h2> <p><span>In response to the growing demand for battery materials, researchers explore alternative resources with a focus on sustainability. Among these, organic electrode materials—including porphyrins—have emerged as promising candidates due to their advantageous properties, such as rapid charging capabilities and high energy densities. However, despite their potential, the precise charging mechanism of these alternatives remains elusive. To address this gap, our study delved into copper porphyrins, with a primary focus on [5,15-bis(ethynyl)-10,20-diphenylporphinato] copper(II) (CuDEPP). Employing synchrotron X-ray absorption spectroscopy in <em>operando</em> mode, we probed the evolution in chemical and electronic structure of Cu in CuDEPP. Our findings unequivocally demonstrate the participation of copper as a redox center during reversible charge storage, shedding light on its superior electrochemical performance. Furthermore, a combined approach involving extended X-ray absorption fine structure (EXAFS) studies and theoretical calculations provided deeper insights into the observed structural distortion during the charge storage process. Notably, our results support the hypothesis that redox processes, specifically those involving the aromatic porphyrin ring, drive the electrochemical activity of CuDEPP. In summary, our investigation offers important insights into the charging mechanism of copper porphyrins—an essential step toward advancing sustainable organic materials for batteries. </span></p>
X-Ray diffraction images for the crystal structure of the motor domain of human kinesin family member 22
<p>This dataset underlies Protein Data Bank entry 3BFN. Diffraction images are accompanied by HKL-3000 data reduction scripts and output files.</p>
Body temperature protein X-ray crystallography at 37°C: A rhenium protein complex seeking a physiological condition structure: Raw Diffraction Images (112 week soak) Zenodo
<p>The labratory dataset of the raw diffraction images obtained after 112 weeks of soaking in the mother liquor and collected at a wavelength of 1.54 Å, illustrating the covalent coordination of the rhenium(I) tricarbonyl fragment to the His and Asp amino acid residues as well as other similarities when comparing the 37°C data set to 100K data set as described in the publication titled "Body temperature protein X-ray crystallography at 37°C: A rhenium protein complex seeking a physiological condition structure", written by Jacobs, Helliwell & Brink,<em> ChemComm</em>, 2024.</p> <p>The raw diffraction images for the labratory data sets are made available at the Zenodo research data archive, as specified in the publication.</p>
FIGURE 8. X-ray images showing internal structures. A in The test architecture of Clypeaster (Echinoidea, Clypeasteroida) and its phylogenetic significance
FIGURE 8. X-ray images showing internal structures. A, Clypeaster reticulatus Agassiz, 1863; NHM 1942.12.26.72. B, Clypeaster australasiae (Gray, 1851); NHM 1952.12.9.8. C, Clypeaster fervens Koehler, 1922; NHM 1948.12.9.17. D, Clypeaster japonicus Döderlein, 1885; NHM EE140012. E, Clypeaster rangianus Desmoulins, 1835; NHM 1957.7.2.48. F, Clypeaster rosaceus Linnaeus, 1758; NHM EE14011.
Fig. 2. X-Ray crystal structures determined for 1,8,9,11,12,14–17,19,20 in Stimulation of insulin secretion by 5-methylcoumarins and its sulfur analogues isolated from Clutia lanceolata Forssk
Fig. 2. X-Ray crystal structures determined for 1,8,9,11,12,14–17,19,20. Atoms are shown as thermal ellipsoids drawn at the 50% probability level.
Data from: New Crystal Forms and Amorphous Phase of Sophoricoside: X-Ray Structures and Characterization
Sophoricoside, which is an isoflavone glycoside found in many plant species, has recently attracted attention because of its anti-fertility activity. One solvent-free form, two solvatomorphs and an amorphous phase of sophoricoside are reported for the first time. X-ray diffractometry, differential scanning calorimetry, thermal gravimetric analysis and Fourier-transform infrared spectroscopy were used to characterize the different forms. The results show that factors such as crystal symmetry, intermolecular arrangement, conformational flexibility, hydrogen-bonding interactions and solvent incorporation lead to different solid-state forms. An investigation of the transformations of the four forms showed that they can interconvert with each other under certain conditions. Amorphous phase and solvatomorphism were unstable but can improve the solubility of sophoricoside in water.
The 1.1 Å Structure of the Periplasmic Phosphate-Binding Protein from Stenotrophomonas maltophilia - a crystallisation contaminant identified by molecular replacement using the entire protein database (X-ray diffraction images).
<p>During efforts to crystallise the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from <em>Alcaligenes</em> sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this structure as the search model did not give a convincing solution with the original atomic resolution dataset. Hence we considered that these crystals might be due to a protein impurity, although molecular replacement using the structures of common crystallisation contaminants as search models again failed. A script to perform molecular replacement using MOLREP (Vagin, A. & Teplyakov, A. (2010). Acta Crystallogr. D 66, 22-25.) in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron density map at 1.1 Å resolution allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate binding protein from <em>Stenotrophomonas maltophilia</em> (UniProt ID: B4SL31; gene ID: Smal_2208) and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked with the virulence of antibiotic resistant strains of pathogenic bacteria and with biofilm formation. The structure has been refined to an R-factor of 10.15 % and an R-free of 12.46 % at 1.1 Å resolution. The molecule adopts the type-II periplasmic binding protein fold with a number of extensively elaborated loop regions. A fully-dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles. </p>
Figures 29-31 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 29-31 - Bembidion alekseevi sp. n., light microscopic images of the holotype. 29 left dorso-lateral aspect 30 right ventro-lateral aspect 31 general view of the amber piece; the position of the fossil is marked by an arrow.
Figures 27-28 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 27-28 - Fossil Bembidion Latreille, 1802, reconstruction of the external shape in dorsal view. 27 B. bukejsi sp. n. 28 B. alekseevi sp. n.
Figures 32-34 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 32-34 - Bembidion alekseevi sp. n., volume rendering of the holotype. 32 dorsal aspect 33 right lateral aspect 34 ventral aspect.
Figures 18-26 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 18-26 - Aedeagal median lobes and endophallic structures of recent Bembidiina (18–25) and the fossil Bembidion bukejsi sp. n. (26), left lateral view. 18 Hoquedela k. kirschenhoferi Müller-Motzfeld, 1988 19 Bembidion (Phyla) tethys Netolitzky, 1926 20 B. (Plataphus) f. fellmanni Mannerheim, 1823 21 B. (Melomalus) altaicum Gebler, 1833 22 B. (Peryphophila) eurydice Andrewes, 1926 23 B. (Andrewesa) patris Schmidt, 2010 24 B. (Bracteon) lapponicum Zetterstedt, 1828 25 B. (Odontium) striatum Fabricius, 1792 26 B. (Eodontium) bukejsi subgen. n., sp. n. (Fig. 26a, volume rendering with highlighted structures, see also Fig. 14; Fig. 26b, schematic reconstruction of putative organization of endophallic structures). Scale bar: 2.2 mm. Abbreviations: bsc = brush sclerite; bsc-fd-av = apico-ventral prolongation of the brush sclerite; csc = central sclerite; csc-ll = left lobe of central sclerite; csc-rl = right lobe of central sclerite; df = dorsal field; dpl = dorsal plate; fl = flagellum of the central fold system; N = N-sclerite (Maddison 2012); of = ostidial flag.
Figures 14-17 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 14-17 - Bembidion bukejsi sp. n., holotype, visualization of endophallic structures using micro-CT. 14 volume rendering of the aedeagal median lobe with sclerotized endophallic structures highlighted in colors 15–16 parts of transverse sections through the abdomen with aedeagus (for position of slices see Fig. 14) 17 sclerotized endophallic structures separated and highlighted in colors using serial sectioning (a-d, left lateral aspect; e, right lateral aspect; f-g, dorsal aspect). Colour coding: beige = internal fold originating from the brush sclerite; green = central sclerite; khaki = dorsal field; light blue = dorsal plate; marine blue = ostidial flag; red = central fold system; white = unknown sclerite; yellow = brush sclerite. Abbreviations: bsc = brush sclerite; bsc-fd-i = internal fold originating from the brush sclerite; bsc-fd-v = ventral prolongation of the brush sclerite; cfd = central folding system; csc = central sclerite; dpl = dorsal plate; mlw = wall of median lobe; scu = unknown sclerite; st = sternite.
Figures 9-13 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 9-13 - Bembidion bukejsi sp. n., holotype, volume rendering of selected body parts 9 caudal aspect of body 10 tarsomeres and distal portion of tibia of right proleg. 11 frontal section of body (ventral aspect) showing position of the abdominal segment IX which surrounds the aedeagus 12 abdominal segment IX and aedeagal median lobe, left lateral aspect 13 sagittal section of aedeagal median lobe, left lateral aspect. Abbreviations: antc = antecosta; bow-l = left wall of basal orfice; bsc-fd = folding structures originating from the endophallic brush sclerite; cfd = central folding system of endophallus; csc = central sclerite of endophallus (left lobe); dpl = dorsal plate of endophallus; mla = aedeagal median lobe apex; mlb = aedeagal median lobe base; mlw-d = dorsal wall of median lobe; mlw-v = ventral wall of median lobe; mtg IX = mediotergite IX; omp = ostial microtrichial patch; pm-l = left paramere (basal portion).
Figures 6-8 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 6-8 - Bembidion bukejsi sp. n., volume rendering of the holotype. 6 dorsal aspect 7 left lateral aspect 8 ventral aspect.
Figures 3-5 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 3-5 - Bembidion bukejsi sp. n., light microscopic images of the holotype. 3 anterior portion of body, dorsal aspect 4 anterior portion of body, ventral aspect 5 left lateral aspect.
Figures 35-36 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 35-36 - Bembidion alekseevi sp. n., volume rendering of the head capsule of the holotype using different grayscale thresholds, dorsal aspect. The arrow in Fig. 36 point to the prominent ridge on internal side of the anterior supraorbital pore, which is characteristic for representatives of the Bembidion subgenus Eupetedromus.
Figures 1-2 from: Schmidt J, Michalik P (2017) The ground beetle genus Bembidion Latreille in Baltic amber: Review of preserved specimens and first 3D reconstruction of endophallic structures using X-ray microscopy (Coleoptera, Carabidae, Bembidiini). ZooKeys 662: 101-126. https://doi.org/10.3897/zookeys.662.12124
Figures 1-2 - Bembidion bukejsi sp. n., light microscopic images of the holotype. 1 dorsal aspect 2 general view of the fossil with contours of the amber piece.
FIGURE 14 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)
FIGURE 14. Line chart of the between-taxa elemental weight percentage comparison. (A) Between taxa comparison within the three gorgonians studied herein (Isis hippuris, Plumigorgia hydroides and Ellisella sp.). (B) Between taxa comparison within the sea pens studied herein (Cavernularia sp., Virgularia sp., and Stylatula sp.).
FIGURE 13 in X-ray Microanalysis and the Chemical Elemental Composition of Gorgonian and Pennatulacean Axial Structures (Anthozoa, Octocorallia)
FIGURE 13. Energy dispersive spectrometer (EDS) area scan dataset. (A) and (B) EDS site of interest BSE image in a higher magnification cross-sectional view of the sea pen Stylatula sp. axial skeleton, acquired by INCA Energy software, partial area scans (spectrum 1 and 4) were applied for between site comparison purpose. Scale bar = 300 μm. (C) and (D) Bar charts of the quantitative results from spectrum 1 and spectrum 4. (E) and (F) EDS results for spectrum 1 and 4.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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