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666 results for “Diffraction”
IODP Expedition 372A X-ray diffraction (XRD)
<p>X-ray diffraction (XRD) is used to identify minerals and their proportions in sediment or hard rock sample powders on a Bruker AXS D4 Endeavor X-ray diffractometer. Results are returned as diffractograms in a viewable format (either PDF or PNG).</p>
IODP Expedition 374 X-ray diffraction (XRD)
<p>X-ray diffraction (XRD) is used to identify minerals and their proportions in sediment or hard rock sample powders on a Bruker AXS D4 Endeavor X-ray diffractometer. Results are returned as diffractograms in a viewable format (either PDF or PNG).</p>
Specimen displacement correction for powder x-ray diffraction in Debye-Scherrer geometry with a flat area detector
<p>This is a repository of synchrotron, powder XRD data including area detector images (.tiff) and integrated intensity vs 2theta files (.xye) for an experiment determining a sample displacement correction equation for powder x-ray diffraction in Debye-Scherrer geometry with a flat area detector. The accuracy of this equation and the corresponding corrections were verified by comparing it with corrections based on finding new integration parameters from an internal standard reference material.</p> <p>This work was published in the Journal of Applied Crystallography, the citation is shown below:</p> <p>Hulbert, B. S. & Kriven, W. M. (2023). J. Appl. Cryst. 56.</p> <p><a href="https://doi.org/10.1107/S1600576722011360">https://doi.org/10.1107/S1600576722011360</a></p>
IODP Expedition 352 X-ray diffraction (XRD)
<p>X-ray diffraction (XRD) is used to identify minerals and their proportions in sediment or hard rock sample powders on a Bruker AXS D4 Endeavor X-ray diffractometer. Results are returned as diffractograms in a viewable format (either PDF or PNG).</p>
IODP Expedition 351 X-ray diffraction (XRD)
<p>X-ray diffraction (XRD) is used to identify minerals and their proportions in sediment or hard rock sample powders on a Bruker AXS D4 Endeavor X-ray diffractometer. Results are returned as diffractograms in a viewable format (either PDF or PNG).</p>
X-ray diffraction images recorded for Aumonier et al., (2022) Slow protein dynamics probed by time-resolved oscillation crystallography at room temperature, IUCrJ
<p>The present repository contains diffraction images corresponding to 27 distinct datasets collected at room temperature on the ESRF beamline ID30A-3 using an Eiger X 4M detector.</p> <p>Datasets have been uploaded with their original names to maintain the metadata integrity. The two following tables match the original names with those attributed in the supplementary table S1 of Aumonier et al., IUCrJ (2022) (https://doi.org/10.1107/S2052252522009150).</p> <table> <tbody> <tr> <td> <p>Data set name on Zenodo</p> </td> <td> <p>X06_01</p> </td> <td> <p>X12_05</p> </td> <td> <p>X07_02_</p> </td> <td> <p>X06_08</p> </td> <td> <p>X14_06</p> </td> <td> <p>X13_03</p> </td> <td> <p>X08_06</p> </td> <td> <p>X11_05</p> </td> <td> <p>X13_05</p> </td> <td> <p>X06_02</p> </td> <td> <p>X11_01</p> </td> <td> <p>X08_01</p> </td> <td> <p>X14_01</p> </td> <td> <p>X13_01</p> </td> <td> <p>X06_03</p> </td> </tr> <tr> <td> <p>Data set in Aumonier et al. 2022</p> </td> <td> <p>Dark</p> </td> <td> <p>PS2</p> </td> <td> <p>PS2</p> </td> <td> <p>PS3</p> </td> <td> <p>PS4</p> </td> <td> <p>PS5</p> </td> <td> <p>PS6</p> </td> <td> <p>PS7</p> </td> <td> <p>R<sub>2”</sub></p> </td> <td> <p>R<sub>3”</sub></p> </td> <td> <p>R<sub>7”</sub></p> </td> <td> <p>R<sub>10”</sub></p> </td> <td> <p>R<sub>13”</sub></p> </td> <td> <p>R<sub>21”</sub></p> </td> <td> <p>R<sub>35”</sub></p> </td> </tr> </tbody> </table> <p> </p> <table> <tbody> <tr> <td> <p>Data set on Zenodo</p> </td> <td> <p>X08_02</p> </td> <td> <p>X11_02</p> </td> <td> <p>X12_02</p> </td> <td> <p>X14_02</p> </td> <td> <p>X13_04</p> </td> <td> <p>X13_02</p> </td> <td> <p>X12_06</p> </td> <td> <p>X06_09</p> </td> <td> <p>X09_04</p> </td> <td> <p>X12_04</p> </td> <td> <p>X06_07</p> </td> <td> <p>X13_07</p> </td> </tr> <tr> <td> <p>Data set in Aumonier et al. 2022</p> </td> <td> <p>R<sub>51”</sub></p> </td> <td> <p>R<sub>62”</sub></p> </td> <td> <p>R<sub>62”</sub></p> </td> <td> <p>R<sub>67”</sub></p> </td> <td> <p>R<sub>72”</sub></p> </td> <td> <p>R<sub>80”</sub></p> </td> <td> <p>R<sub>90”</sub></p> </td> <td> <p>R<sub>130”</sub></p> </td> <td> <p>R<sub>166”</sub></p> </td> <td> <p>R<sub>258”</sub></p> </td> <td> <p>R<sub>630”</sub></p> </td> <td> <p>R<sub>1620”</sub></p> </td> </tr> </tbody> </table> <p>One dataset consists of a master file, four data files and two metadata files.</p>
Crystal structure of a 1:1 cocrystal of OPC-167832 with 2,5-dihydroxybenzoic acid using microcrystal electron diffraction
<p>The title cocrystal, OPC-167832 (5-(((3R,4R)-1-(4-chloro-2,6-difluorophenyl)-3,4-dihydroxypiperidin-4-yl)methoxy)-8-fluoro-3,4-dihydroquinolin-2(1H)-one); C<sub>21</sub>H<sub>20</sub>ClF<sub>3</sub>N<sub>2</sub>O<sub>4</sub>) and 2,5-dihydroxybenzoic acid (2,5DHBA; C<sub>7</sub>H<sub>6</sub>O<sub>4</sub>) were successfully cocrystallized and the crystal structure was solved via microcrystal electron diffraction.</p>
Raw diffraction images of lysophosphatidic acid receptor LPA6
<p>LPA<sub>6</sub> is a class A G protein-coupled receptor which recognizes lysophosphatidic acid, a lipid mediator, as its ligand. The crystallization construct consists of zebrafish lysophosphatidic acid receptor LPA<sub>6</sub> and T4 lysozyme fused within the intracellular loop 3 of LPA<sub>6</sub>. The crystals were obtained within the lipidic cubic phase. No synthetic chemical compounds were added for the crystallization.</p> <p>397 small-wedge (4° or 6°/crystal) datasets collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. The crystals belonged to space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> with unit cell parameters a=55.9, b=65.0, c=160.7 Å.</p> <p>241 datasets were merged at 3.2 Å resolution in the published result (Taniguchi et al. Nature 2017; PDB code: 5XSZ) using KAMO; see processing note https://github.com/keitaroyam/yamtbx/wiki/Processing-LPA6-data-(5XSZ)</p> <p>NOTE</p> <ul> <li> <p>flatfield correction was not applied to the images and you need to apply it using the correction table saved in master.h5 files.</p> </li> <li> <p>master.h5 files were modified; see https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md</p> </li> <li> <p>Most frames have lipid rings and some have ice rings.</p> </li> </ul>
Raw diffraction images of endothelin ETB receptor bound to clinical antagonist bosentan and its analog
<p>Diffraction images of endothelin ET<sub>B</sub> receptor bound to bosentan (PDB code 5XPR) and K-8794 (5X93).</p> <p>Bosentan is an oral medication approved for the treatment of pulmonary arterial hypertension. K-8794 is the ETB-selective high-affinity analog of bosentan.</p> <p>Two datasets of 5X93 were collected with helical method, while for 5XPR 16 small-wedge (10°/crystal) datasets were collected automatically using ZOO system. In both cases the diffraction images were collected from loop-harvested microcrystals using MX225HS CCD detector at a wavelength of 1 Å on BL32XU, SPring-8.</p> <p>For 5XPR, 14 datasets were merged at 3.6 Å resolution in the published result (Shihoya et al. NSMB 2017) using KAMO; see processing note: https://github.com/keitaroyam/yamtbx/wiki/Processing-ETBR-bonsentan-data-(5XPR)</p> <p>NOTE</p> <ul> <li> <p>Most frames have (relatively weak) lipid rings.</p> </li> </ul> <ul> <li> <p>There is the indexing ambiguity problem in 5XPR (space group P3<sub>2</sub>21) that should be resolved before merging.</p> </li> <li> <p>5xpr_bosentan/bosentan-1425-01/multi_002_000019.img.bz2 is missing (probably due to a detector problem)</p> </li> </ul>
Single Crystal X-ray diffraction data for D-phgAT
<p>Single Crystal X-ray diffraction data for Dpg-AT from <em>Pseudomonas stutzeri. </em>Data collected at Diamond Light Source, on beamline I03 on 18/02/2017.</p>
Raw diffraction images of eukaryotic MATE transporter (AtDTX14)
<p>Multidrug And Toxic compound Extrusion (MATE) transporter exports xenobiotics by using the gradient of H<sup>+</sup>. The crystals were obtained within the lipidic cubic phase.</p> <p>288+85 (Auto+manual) small-wedge (5-20°/crystal) datasets collected from loop-harvested microcrystals using MX225HS CCD detector at a wavelength of 1 Å on BL32XU, SPring-8. The crystals belonged to space group P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> with unit cell parameters a=52.8, b=86.8, c=116.4 Å.</p> <p>100 datasets were merged at 2.6 Å resolution in the published result (Miyauchi et al. Nature Communications, 2017; PDB code: 5Y50) using KAMO; see processing note https://github.com/keitaroyam/yamtbx/wiki/Processing-AtDTX14-data-(5Y50)</p> <p>Note that most frames have lipid rings.</p>
Raw diffraction images of human orexin 2 receptor bound to the subtype-selective antagonist EMPA
<p>Human orexin 2 receptor (OX2R) is a member of G protein-coupled receptors (GPCR). OX2R plays important roles in modulating feeding behavior and regulating the sleep-wake cycle.</p> <p>805 small-wedge (1-6°/crystal) datasets collected from loop-harvested microcrystals using MX225HS CCD detector at a wavelength of 1 Å on BL32XU, SPring-8. The crystals belonged to space group C2 with unit cell parameters a=94.1, b=75.5, c=95.9 Å, β=111.4°.</p> <p>631 datasets were merged at 1.96 Å resolution in the published result (Suno et al. Structure 2017; PDB code: 5WQC) using KAMO; see https://github.com/keitaroyam/yamtbx/wiki/Processing-OX2R-data-(5WQC)</p> <p>Note</p> <ul> <li>Most frames have lipid rings.</li> <li>One dataset (not included in the published result) was lost for some reason (so 804 datasets are available).</li> </ul>
Raw diffraction images of leukotriene B4 receptor BLT1
<p>Diffraction images of Leukotriene B<sub>4</sub> receptor (BLT1) in complex with antagonist BIIL260, a chemical bearing a benzamidine moiety. BLT1 is one of class-A G-protein coupled receptor (GPCR), and the bound benzamidine moiety mimics a sodium ion-centered water cluster of BLT1 that is considered to exist in many class-A GPCRs. The bound benzamidine moiety stabilizes the inactive state of BLT1, and BIIL260 exhibits the characteristics of an inverse agonist for BLT1.</p> <p>Small-wedge (1296 crystals, 2.5°/crystal) datasets collected from loop-harvested microcrystals using EIGER X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. The crystals belonged to space group P22<sub>1</sub>2<sub>1</sub> with unit cell parameters a=69.6, b=77.6, c=135.5 Å.</p> <p>Finally, 494 datasets were merged at 3.7 Å resolution in the published result (Hori et al. Nature Chemical Biology, 2018; PDB code: 5X33) using KAMO; see processing note https://github.com/keitaroyam/yamtbx/wiki/Processing-BLT1-data-(5X33)</p> <p>Note</p> <ul> <li>The master.h5 files were modified; see https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md</li> <li>To further reduce total file size, flatfield data of master.h5 were removed and saved in a file in each directory (linked from master.h5 files).</li> <li>Most frames have lipid rings.</li> </ul>
Electron Backscatter Diffraction Patterns from Titanium-added Interstitial-free Steel Containing Subgrains
<h3><strong>Associated Publications</strong></h3> <ol> <li>Bennett IV, T.J. and Taleff, E.M. Dynamic Grain Growth Driven by Subgrain Boundaries in an Interstitial-Free Steel During Deformation at 850 °C. <em>Metall Mater Trans A</em> 55, 429–446 (2024). <a href="https://doi.org/10.1007/s11661-023-07256-w">https://doi.org/10.1007/s11661-023-07256-w</a>.</li> <li>Bennett IV, T.J. and Taleff, E.M. Imaging and Segmenting Grains and Subgrains using Backscattered Electron Techniques. Under review (2024).</li> </ol> <h3><strong>Data Description</strong></h3> <p>These data were collected by Thomas J. Bennett IV on July 28, 2022.</p> <p>The electron backscatter diffraction (EBSD) data and associated electron backscatter diffraction patterns (EBSPs) contained herein were acquired from a titanium-added interstitial-free (Ti-IF) steel sheet material containing numerous subgrains. The Ti-IF steel specimen that provided these data was ramped to 850 degrees Celsius over 30 minutes, held at this temperature for one hour, and then deformed at a constant true-strain rate of 10^-4 s^-1. Upon reaching a final true strain of 0.225, the specimen was air quenched while maintaining a constant stress to preserve subgrains formed during high-temperature deformation. The tensile specimen was cut from a Ti-IF steel sheet received in a hard as-rolled condition with the tensile axis parallel to the sheet rolling direction. EBSPs were acquired from a section cut from the center of the deformed gage region using a JEOL JSM-IT300HR SEM equipped with an EDAX Velocity EBSD camera at the Center for Integrated Nanotechnologies.</p> <p>The following conditions were used for EBSD data acquisition:</p> <table> <tbody> <tr> <td>Accelerating Voltage:</td> <td>20 kV</td> </tr> <tr> <td>Beam Current:</td> <td>80%</td> </tr> <tr> <td>Working Distance:</td> <td>20.0 mm</td> </tr> <tr> <td>Magnification:</td> <td>200×</td> </tr> <tr> <td>Dynamic Focus:</td> <td>44 (out of 255, arbitrary units)</td> </tr> <tr> <td>Specimen Tilt:</td> <td>70 degrees</td> </tr> <tr> <td>Scanning Grid Type:</td> <td>Square</td> </tr> <tr> <td>Step Size (x and y):</td> <td>0.5 μm</td> </tr> <tr> <td>Scan Size:</td> <td>520 (across) × 340 (down) pixels</td> </tr> <tr> <td>EBSD Camera Resolution:</td> <td>446 × 446 pixels</td> </tr> <tr> <td>EBSD Camera Binning:</td> <td>1 × 1</td> </tr> <tr> <td>EBSD Camera Exposure Time:</td> <td>10 ms</td> </tr> <tr> <td>Frame Averaging:</td> <td>None</td> </tr> <tr> <td>Specimen Tensile Direction:</td> <td>Horizontal</td> </tr> <tr> <td>Specimen Rolling Direction:</td> <td>Horizontal</td> </tr> <tr> <td>Specimen Long Transverse Direction:</td> <td>Vertical</td> </tr> <tr> <td>Specimen Short Transverse Direction:</td> <td>Normal to plane</td> </tr> <tr> <td>Pattern Center (EMSphInx Convention):</td> <td>(x_pc, y_pc, L) = (-0.2 pixels, 112.76 pixels, 21736.4 μm)</td> </tr> <tr> <td>EBSD Camera Elevation Angle:</td> <td>3 degrees</td> </tr> <tr> <td>EBSD Camera Screen Width:</td> <td>32 mm</td> </tr> <tr> <td>Pixel size on EBSD Camera Screen:</td> <td>71.749 μm/pixel ( = 32000 μm / 446 pixels)</td> </tr> </tbody> </table> <p> </p> <p><em>Note:</em> Conversions between different pattern center conventions may be found in the journal article below or at the following link: <a href="https://github.com/EMsoft-org/EMsoft/wiki/DItutorial">https://github.com/EMsoft-org/EMsoft/wiki/DItutorial</a>.</p> <ul> <li>Jackson, M.A., Pascal, E., and De Graef, M. Dictionary Indexing of Electron Back-Scatter Diffraction Patterns: a Hands-On Tutorial. <em>Integr Mater Manuf Innov</em> 8, 226–246 (2019). <a href="https://doi.org/10.1007/s40192-019-00137-4">https://doi.org/10.1007/s40192-019-00137-4</a>.</li> </ul> <h3><strong>File Descriptions</strong></h3> <ul> <li>Specimen_orientation.pdf - A schematic showing specimen reference directions and the orientation used for EBSD data acquisition.</li> <li>Patterns.zip - A compressed archive containing Patterns.up2. This file contains 16-bit EBSPs and is 70,336,697,616 bytes (70.3 GB) uncompressed.</li> <li>SHT_Indexed.ang - A file containing orientation data produced by indexing Patterns.up2 using EMSphInx. Orientations are represented by Euler angles (Bunge convention) and are to be interpreted using the EDAX Setting 2 convention (see MTEX documentation at <a href="https://mtex-toolbox.github.io/EBSDReferenceFrame.html">https://mtex-toolbox.github.io/EBSDReferenceFrame.html</a>).</li> <li>SHT_Indexed.h5 - A file in HDF5 format containing orientation data and other relevant information produced by indexing Patterns.up2 using EMSphInx.</li> <li>SHT_Indexed_IPFmap.png - An image of an inverse pole figure map colored with respect to the short transverse direction showing the data from SHT_Indexed.ang.</li> </ul> <p><em>Note:</em> The basic format of "up2" files is the following. The first 4 bytes provide the version number. The second 4 bytes are the width of the patterns. The third 4 bytes are the height of the patterns. The fourth 4 bytes are the starting position of the pattern image data.</p> <h3><strong>Acknowledgments</strong></h3> <p>The authors gratefully acknowledge support from the National Science Foundation under Grant DMR-2003312 and instrumentation under Grant DMR-9974476. The authors also gratefully acknowledge support from the U.S. Department of Energy, Office of High Energy Physics under Grant DE-SC0009960. This work was performed, in part, at the Center for Integrated Nanotechnologies, an Office of Science User Facility operated for the U.S. Department of Energy (DOE) Office of Science by Los Alamos National Laboratory (Contract 89233218CNA000001) and Sandia National Laboratories (Contract DE-NA-0003525). The authors thank Mr. Thomas Cayia (Arcelor Mittal) for providing the interstitial-free steel material used for this study.</p>
X-ray diffraction data set for PDB 9G3L: LecB from PA01 in complex with beta-fucosylamide-indole derivative
<p>X-ray diffraction images collected on proxima 1 Soleil the 7th of march 2024 at SOLEIL synchrotron, Saint Aubin, France for PDB ID 9G3L using a DECTRIS EIGER X 16M detector. X-ray dataset and xdsme processing for the structure of LecB from <em>Pseudomonas aeruginosa</em> PA01 strain in complex with synthetic beta-fucosylamide-indole derivative. Images 1-900 were removed during processing and resolution was cut to 1.74 angstrom.</p>
X-ray diffraction dataset for PDB 9G3K LecB from PA01 in complex with synthetic beta-fucosylamide
<p>X-ray diffraction images collected on proxima 2 Soleil the 17th of november 2023 at SOLEIL synchrotron, Saint Aubin, France for PDB ID 9G3K using a DECTRIS EIGER X 9M detector. X-ray dataset and xdsme processing for the structure of LecB from Pseudomonas aeruginosa PA01 strain in complex with synthetic beta-fucosylamide-furan-phenyl derivative. Data were cut at 1.55 A.</p>
Selenomethionine MAD diffraction images for calexcitin.
<p>The selenomethionine multiwavelength anomalous dispersion (MAD) data used to solve the structure of Loligo Pealei calexcitin. Data were collected at beamline BM16, ESRF Grenoble, France (c/o Dr Gavin Fox) and details are given in the scanned notes included. </p>
Diffraction images used for refinement of calexcitin.
<p>Diffraction images used for high resolution refinement of the X-ray structure of <em>Loligo pealei</em> calexcitin. The data were collected at beamline ID14-1 at ESRF, Grenoble. Details of the data collection can be found in the scanned notebook pages. </p>
Multiwavelength anomalous dispersion (MAD) diffraction images of Burkholderia pseudomallei BipD.
<p>Selenomethionine MAD diffraction images from beamline BM16 at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) that were used for structure analysis of BipD from <em>Burkholderia pseudomallei</em>. Details of the data collection are given in the included scanned notes. </p>
Transthyretin Eiger 9M X-ray diffraction dataset
<p>Transthyretin X-ray diffraction dataset collected during commissioning of Eiger 9M detector on Proxima2A beamline, Synchrotron SOLEIL, France.</p>
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