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169 results for “Diffraction images”
Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (Proline-serine-threonine phosphatase-interacting protein 1) (PDB entry 7AAN)
<p>Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (residues 1-289).</p> <p>Data were collected on a single crystal at the beamline i03 of the Diamond Light Source synchrotron (Didcot, UK) using radiation of 0.99987 Å wavelength and a PILATUS3 6M detector. The dataset consists of 3600 images (0.15 degree oscillation per image) that were collected: 2400 at one position and the other 1200 at a second site in the same crystal. Crystal belongs to the space group P2(1)2(1)2(1) with unit cell dimensions a=48.3 Å, b=71.9 Å, c=204.6 Å. The asymmetric unit contains an homodimer of the F-BAR domain (~53% solvent content), which is the biological unit.</p> <p>Diffraction data was notably anisotropic. The lowest resolution limit was 4.32 Å in the direction b* and the highest limits were 2.12 Å and 2.17 in the directions a* and c*, respectively.</p> <p>The structure derived form these data is published in:</p> <p>Manso, J.A., Marcos, T., Ruiz-Martín, V. Casas J, Alcón P, Sánchez Crespo M, Bayón Y, de Pereda JM, Alonso A <em>PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders</em>. <strong>Cell. Mol. Life Sci</strong>. 79, 131 (2022). <a href="https://doi.org/10.1007/s00018-022-04173-w">https://doi.org/10.1007/s00018-022-04173-w</a></p> <p>The structure is available at the PDB under the code <strong>7AAN</strong>:</p> <p><a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7aan">https://www.ebi.ac.uk/pdbe/entry/pdb/7aan</a></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>
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>
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>
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>
Diffraction images of a crystal of the complex formed by fragments of the integrin beta4 and the bullous pemphigoid antigen 1 (BP230, BPAG1e). PDB entry 6GVL.
<p>Data were collected on a single crystal at the beamline i03 of the Diamond synchrotron facility (Didcot, UK) using radiation of 0.97625 Å wavelength and a PILATUS3 6M detector. The dataset consists of 2400 images (0.15 degree oscillation per image).</p>
Diffraction images of a crystal of the complex formed by fragments of the integrin beta4 and the bullous pemphigoid antigen 1 (BP230, BPAG1e). Integrin high affinity point mutant. PDB entry 6GVK.
<p>Data were collected on a single crystal at the beamline XALOC of the ALBA-CELLS synchrotron facility (Cerdanyola del Vallés, Barcelona, Spain) using radiation of 0.97915 Å wavelength and a PILATUS 6M detector. The complete dataset is build up of three sub-sets measured at three different positions of a single crystal. Each sub-set consists of 1800 images (0.2 degree oscillation per image).</p>
Single crystal diffraction images for a room temperature data collection on the LEF-PG co-crystal.
<p>A set of diffraction images collected on a Rigaku FRE+ diffractometer, equipped with HF Varimax confocal mirrors and an AFC12 goniometer and HG Saturn 724+ detector diffractometer.</p> <p>The sample is an organic co-crystal that forms part of a study of the LEF active pharmaceutical ingredient with a range of coformers. The structure with the PG coformer shows strong signs of modulation in the diffraction pattern and structure refinement. The model presented in the paper (submitted to Crystal Growth and Design) does not account for any modulation and serves the purpose of a suitable degree of characterisation precision for this article. </p> <p>The authors wish to make the raw data available so that those with interest and experise in handling modulated structures can perform more detailed modelling studies and/or use the data to test software or for training examples.</p>
Raw diffraction images of heliorhodopsin
<p>Crystal structure of heliorhodopsin from <em>Thermoplasmatales archaeon </em>(PDB code: <a href="https://www.rcsb.org/structure/6IS6">6IS6</a>).</p> <p>Small-wedge (10-15°/crystal) datasets collected from loop-harvested microcrystals using <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md">EIGER</a> X 9M detector at a wavelength of 1 Å on BL32XU, SPring-8. Beam size was around 15×10 µm<sup>2</sup> and oscillation step was 0.1°. The crystals belonged to space group C222<sub>1</sub> with unit cell parameters a~52, b~110, c~108 Å.</p> <p>In total 212 small-wedge and two helical (180 & 120°) datasets were collected, and of these 179 datasets were indexed and integrated using XDS with <a href="https://github.com/keitaroyam/yamtbx/blob/master/doc/kamo-en.md">KAMO</a> pipeline. Finally 107 integrated results were merged at 2.4 Å resolution after CC-based clustering and outlier rejection by KAMO in the published result (Shihoya et al. Nature, 2019).</p> <p>This upload also includes SeMet-labeled heliorhodopsin data (not actually used for phasing) and a different crystal form (tetragonal). SeMet data could be merged in P2<sub>1</sub>2<sub>1</sub>2<sub>1</sub> space group at 3.8 Å resolution. The tetragonal data are at 2.8 Å resolution.</p>
ptychographic_diffraction_image_sets_20211026
<p>121 spiral scans with 963 images each</p> <p>using a medipix3 detector with 55 um pixelsize and at 1.55 m downstream of the samples</p> <p>step size is 50 nm per scan with 0.4 s exposure time</p> <p>beam position is included in positions.csv</p> <p> </p>
Volumetric segmentation of biological cells and subcellular structures for optical diffraction tomography images - dataset
<p>This dataset includes 4 files with segmentation results for 4 different ODT reconstructions of SH-SY5Y neuroblastoma cell. The segmentation results contain:</p> <ol> <li>3D binary masks of biological cells obtained through Cellpose [1] and <a href="https://github.com/biopto/ODT-SAS.git">ODT-SAS</a>;</li> <li>3D binary masks of organelles: nucleoli and lipid structures (LS) obtained through slice-by-slice manual segmentation and ODT-SAS.</li> </ol> <p>All files are .*mat files.</p> <p>The files <em>REC_SH-SY5Y_1.mat, REC_SH-SY5Y_2.mat</em> and<em> REC_SH-SY5Y_3.mat</em> consist of 7 variables:</p> <p>RECON – tomographic reconstruction of SH-SY5Y neuroblastoma cell;<br> n_imm – refractive index of object immersion medium;<br> dx – object space sample size in XY [<span class="math-tex">\(\mu m\)</span>];<br> rayXY – xy-coordinates of illumination vectors;</p> <p>maskManual – table with manually determined 3D binary masks of organelles;<br> maskCellpose – 3D binary mask of biological cell obtained through Cellpose;<br> maskODTSAS – table with 3D binary masks of biological cell and their organelles obtained through ODT-SAS.</p> <p>File <em>REC_SH-SY5Y_4.mat</em> includes masks for the ODT-SAS and Cellpose segmentation of three closely packed cells and consists of 5 variables: RECON, n_imm, dx, maskCellpose and maskODTSAS.<br> <br> Access a particular 3D binary mask from 'maskManual' and 'maskODTSAS' tables, using the following names: 'Cell', 'Nucleoli', 'LS'.<br> For example:</p> <pre><code>cellMask = maskODTSAS.Cell{1};</code></pre> <p><br> [1] Stringer, C., Wang, T., Michaelos, M., & Pachitariu, M. (2021). Cellpose: a generalist algorithm for cellular segmentation. Nature methods, 18(1), 100-106.</p> <p> </p>
Raw Data: Magnetostrictive FeCoSiB coated ZnO Microstructures by Bragg Coherent X-Ray Diffraction Imaging
<p>Five sets of raw data from (Fe<sub>90</sub>Co<sub>10</sub>)<sub>78</sub>Si<sub>12</sub>B<sub>10</sub> coated ZnO microstructure (rod) investigated by Bragg coherent X-ray diffraction imaging. FeCoSiB is a magnetostrictive alloy, thus a changing strain is expected for applied magnetic fields.</p> <p>Included is data from the same spatial positions along the c-axis of the ZnO rod at five different magnetic flux densities [0, 4.4, 5.6, 9.1, 13.2]/mT. Futher on called P1 to P5. For each position there is a .nxs file of a rocking scan around the {0001} Bragg reflection, collected by a 2D detector and other recorded values, e.g. motor positions, counter values. </p>
X-ray diffraction images of the beta4 tetramer of the C-terminal peptide of the split chain transketolase
<p>X-ray images for PDB entry 6YAJ</p> <p>DOI for the pdb is https://doi.org/10.2210/pdb6YAJ/pdb</p> <p>Title: A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans : Structure and Biochemical Characterization.<br> Journal: Front Microbiol<br> Volume: 11<br> Pages: 592353 - 592353<br> Year: 2020<br> PubMed ID: 33193259<br> DOI: 10.33 89/fmicb .2020.592353</p> <p> </p> <p> </p>
X-ray diffraction images of the alpah2beta2 heterotetramer of the split chain transketolase
<p>Data were collected on Diamond I04-1 14 Dec 2013.</p> <p> James, P.,Isupov, M.N.,De Rose, S.A.,Sayer, C.,Cole, I.S.,Littlechild, J.A.<br> <br> A 'Split-Gene' Transketolase From the Hyper-Thermophilic Bacterium Carboxydothermus hydrogenoformans : Structure and Biochemical Characterization.<br> <br> Journal: Front Microbiol<br> Volume: 11<br> Pages: 592353 - 592353<br> Year: 2020<br> PubMed ID : 3319 3259<br> DOI: 10.3389/fmicb.2020.592353<br> <br> PDB DOI: https://doi.org/10.2210/pdb6YAK/pdb</p>
X-ray diffraction images for DPF3 tandem PHD fingers co-crystallized with an acetylated histone-derived peptide
<p>This submission includes a tar archive of bzipped diffraction images recorded with the ADSC Q315r detector at the Advanced Photon Source of Argonne National Laboratory, Structural Biology Center beam line 19-ID. Relevant meta data can be found in the headers of those diffraction images.</p> <p>Please find below the content of an input file XDS.INP for the program XDS (Kabsch, 2010), which may be used for data reduction. The "NAME_TEMPLATE_OF_DATA_FRAMES=" item inside XDS.INP may need to be edited to point to the location of the downloaded and untarred images.</p> <p>!!! Paste lines below in to a file named XDS.INP</p> <p>DETECTOR=ADSC MINIMUM_VALID_PIXEL_VALUE=1 OVERLOAD= 65000<br /> DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0<br /> DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0<br /> TRUSTED_REGION=0.0 1.05<br /> MAXIMUM_NUMBER_OF_JOBS=10<br /> ORGX= 1582.82 ORGY= 1485.54<br /> DETECTOR_DISTANCE= 150<br /> ROTATION_AXIS= -1.0 0.0 0.0<br /> OSCILLATION_RANGE=1<br /> X-RAY_WAVELENGTH= 1.2821511<br /> INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0<br /> FRACTION_OF_POLARIZATION=0.90<br /> POLARIZATION_PLANE_NORMAL= 0.0 1.0 0.0<br /> SPACE_GROUP_NUMBER=20<br /> UNIT_CELL_CONSTANTS= 100.030 121.697 56.554 90.000 90.000 90.000<br /> DATA_RANGE=1 180<br /> BACKGROUND_RANGE=1 6<br /> SPOT_RANGE=1 3<br /> SPOT_RANGE=31 33<br /> MAX_CELL_AXIS_ERROR=0.03<br /> MAX_CELL_ANGLE_ERROR=2.0<br /> TEST_RESOLUTION_RANGE=8.0 3.8<br /> MIN_RFL_Rmeas= 50<br /> MAX_FAC_Rmeas=2.0<br /> VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS= 6000 30000<br /> INCLUDE_RESOLUTION_RANGE=50.0 1.7<br /> FRIEDEL'S_LAW= FALSE<br /> STARTING_ANGLE= -100 STARTING_FRAME=1<br /> NAME_TEMPLATE_OF_DATA_FRAMES= ../x247398/t1.0???.img</p> <p>!!! End of XDS.INP</p> <p> </p> <p> </p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.