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60 results for “crystallography”
Discrimination of aluminum from silicon by electron crystallography with the JUNGFRAU detector
<p>Electron diffraction data of two different aluminosilicates, zeolite A and albite. They were used to implement the JUNGFRAU detector (PSI Switzerland) at Vienna University, and develop the software for data conversion and data collection. The archives also contain the XDS files for processing. The metadata of the CBF-files mostly not filled in properly (pixel size and wavelength only are correct). Please refer to the XDS.INP files for experimental parameters (oscillation width, detector distance, etc.). The structural CIF files have been submitted to the Cambridge Structural Database CSD.</p>
Serial synchrotron crystallography dataset and 3D-ED dataset - HEWL crystals obtained by instant crystallization with TbXo4
<h2>Data sets related to the publication "Nucleating Agent Crystallophore Induces Instant Protein Crystallization" by Sauter et al.</h2> <p><em><strong>3D-Electron Diffraction data</strong></em>: The raw data obtained on the protein Hen Egg-White Lysozyme is contained in the file <em>RAW-Data_3D-ED_deposition.tar.bz2</em>.</p> <p>Results of first rounds of model refinement are contained in <em>3D-ED-affi_4-5sets</em> files</p> <p><em><strong>Synchrotron Serial Crystallography data</strong></em>: The raw SSX data obtained on the protein Hen Egg-White Lysozyme can be accessed through <a href="https://doi.org/10.15151/ESRF-DC-1823716276">https://doi.org/10.15151/ESRF-DC-1823716276</a>.</p> <p>Results of first rounds of model refinement are contained in <em>SSX-Xo4-supernatent</em> files</p>
SDF format of Crystallography Open Database - April 2023
<p>This is a dump & transform to SDF of the crystallography open database that I computed & published in the context of a blog post. You can use that as alternative to extract angle, dihedral or distance statistics from freely & openly accessible crystal structures. </p>
Diffraction data underpinning the structure of StayGold determined by X-ray crystallography (PDB code 8BXT)
<p>Raw diffraction data underpinning the crystal structure of StayGold fluorescent protein.</p> <p>This is the raw data underpinning PDB entry 8BXT.</p>
Analysis of insulin glulisine at the molecular level by X-ray crystallography and biophysical techniques
<p>Raw diffraction images for the study:- Gillis, R.B., Solomon, H.V., Govada, L. <em>et al.</em> Analysis of insulin glulisine at the molecular level by X-ray crystallography and biophysical techniques. <em>Sci Rep</em> <strong>11, </strong>1737 (2021). https://doi.org/10.1038/s41598-021-81251-2 </p> <p>PDB code 6GV0.</p>
Serial Crystallography with Multi-stage Merging oi 1000's of Images
<p>In the associated paper we discuss the issues involved in improving the sensitivity of both approaches to clustering, using, as an example, 999 5 degree wedges from lysozyme in four iso-forms:</p> <p> NAG: native with N-acetylglucosamine (NAG) soaked in,<br> benzamadine: native with benzamadine soaked in,<br> benzamadine plus NAG: native with both NAG and benzamadine soaked in.<br> Native: no ligands</p> <p>Although the cell parameters are changed sufficiently to allow recognition of the NAG soak, it is difficult to filter the benzamadine soak simply on the basis of cell parameter changes, suggesting the desirability of switching from cell-based clustering to reflection-based clustering as early in the process as possible. </p> <p>The data is this dataset consists of a bzipped HKL structure factor tarball and a bzipped cluster data files from the four forms tarball.</p>
Data from: Comparative crystallography suggests Maniraptoran theropod affinities for latest cretaceous European 'geckoid' eggshell
<p>Thin fossil eggshells from Upper Cretaceous deposits of Europe, characterized by nodular ornamentation similar to modern gekkotan eggshells, have mostly been interpreted as gekkotan (='geckoid') in origin. However, in some cases, like the oogenus Pseudogeckoolithus, their theropod affinity was also suggested. The true affinity of these fossil 'geckoid' eggshells remained controversial due to the absence of analytical methods effective in identifying genuine gecko eggshells in the fossil record. In this study, we apply electron backscatter diffraction (EBSD) analysis to latest Cretaceous European 'geckoid' (including Pseudogeckoolithus) eggshells, in comparison with modern gekkotan and theropod (avian) eggshells. Our results show that Pseudogeckoolithus has a definite theropod eggshell-like crystallographic configuration, in clear contrast to that seen in modern geckos. Furthermore, the crystallography of the nodular ornamentation in Pseudogeckoolithus is comparable to that seen in megapode eggshells, but different from that of gecko eggshells, despite superficial morphological similarity. The remarkable morphological similarities between Pseudogeckoolithus and modern gecko eggshells are thus convergent, and the 'gekkotan affinity' hypothesis can be dismissed for Pseudogeckoolithus. This study provides a template for differentiating true gekkotan from dinosaurian eggshells in the fossil record. The potential functional significance of eggshell ornamentation, lost in most modern birds, requires further study, and experimental zoological approach may shed light on this issue. Finally, our results caution about the dangers of using potentially homoplastic eggshell characters in eggshell parataxonomy.</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>
Electron crystallography with the EIGER detector
<p>Electron diffraction data as part of the publiation https://doi.org/10.1107/S2052252518000945https://doi.org/10.1107/S2052252518000945; Data set with 25keV Threshold. For experimental details see XDS.INP file.</p>
Electron crystallography with the EIGER detector
<p>Electron diffraction data as part of the publiation https://doi.org/10.1107/S2052252518000945https://doi.org/10.1107/S2052252518000945; Data set with 60keV Threshold. For experimental details see XDS.INP file.</p>
Radiation Damage in Small Molecule Crystallography - Experiment 6
<p>Sixth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.9889 Angstrom</p> <p>Temperature: 30 K</p> <p>Flux: 2.627•10<sup>10 </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 1.90 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 5
<p>Fifth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.9028 Angstrom</p> <p>Temperature: 100K</p> <p>Flux: 6.605•10<sup>9 </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 0.79 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 3
<p>Third data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100K</p> <p>Flux: 4.35•109<sup> </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 0.32 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 8
<p>Eighth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 120 K</p> <p>Flux: 8.42•109<sup> </sup>ph/s</p> <p>Crystal size: 0.050 x 0.010 x 0.010 mm</p> <p>Calculated dose (DWD) per scan: 0.60 MGy</p>
Radiation damage in small molecule crystallography - experiment 1
<p>First data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100 K</p> <p>Flux: 8.8•10<sup>9 </sup>ph/s</p> <p>Crystal size: 0.050 x 0.010 x 0.010 mm</p> <p>Calculated dose (DWD) per scan: 0.63 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 4
<p>Fourth data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100K</p> <p>Flux: 8.162•10<sup>9 </sup>ph/s</p> <p>Calculated dose (average DWD) per scan: 0.57 MGy</p>
Radiation Damage in Small Molecule Crystallography - Experiment 2
<p>Second data set in a series of experiments investigating the effect of radiation damage to a small molecule crystal structure.</p> <p>Sample: catena-(bis(m2-Glycyl-histidinato-N,N',O)-nickel(II) heptahydrate)</p> <p>sum formula: C16H36N8NiO13</p> <p>Wavelength: 0.6889 Angstrom</p> <p>Temperature: 100 K</p> <p>Flux: 1.73•10<sup>10 </sup>ph/s</p> <p>Crystal size: 0.050 x 0.010 x 0.010 mm</p> <p>Calculated dose (average DWD) per scan: 1.27 MGy</p>
3D-structured Supports create complete Data Sets for Electron Crystallography
<p>Each tar file contains the raw files in HDF5 format, together with the XDS.INP file used for data integration.</p> <p>NB: The meta-data in the HDF5 files have no meaning, please refer to the respective XDS.INP file for respective information.</p>
Examples of applying a multivariate Wilson prior to comparative crystallography data
<p>This folder contains four examples of merging crystallographic intensities with a bivariate prior:</p> <ul> <li>time-resolved Laue crystallography of the photoactive yellow protein (pyp.zip)</li> <li>anomalous diffraction from serial XFEL crystallography of thermolysin (thermolysin_xfel.zip)</li> <li>anomalous diffraction from Laue crystallography of NaI-soaked lysozyme (lysozyme.zip)</li> <li>fragment screening monochromatic data of Nsp3 Mac1 (dfs.zip)</li> </ul> <p>Additionally, we provide several auxilliary examples:</p> <ul> <li>For PYP, an example where we set aside a test fraction to semi-independently optimize the double-Wilson r (pyp_test_fraction.zip)</li> <li>for lysozyme, two examples, one where we use Laue-DIALS instead of precognition (lysozyme-laue-dials.zip), and another where we set aside the first 90 images to semi-independently optimize the double-Wilson r (lysozyme_test_fraction.zip)</li> <li>For thermolysin, an example where we use a bivariate versus a univariate prior as the number of scaled images grows (thermolysin_xfel_frames_sweep.zip), and another where we set aside the first 395 images to semi-independently optimize the double-Wilson r (thermolysin_xfel_test_fraction.zip)</li> </ul> <p>Finally, we provide zip files containing Careless repositories (careless_041.zip, careless_053.zip) and the <a href="https://github.com/Hekstra-Lab/dw">dw</a> repository containing Jupyter notebooks outlining the theory of the double-Wilson model (dw.zip).</p> <p>Every example includes scripts to run Careless as well as to analyze the outputs in order to reproduce the figures in the double-Wilson manuscript. For every example, there is a `README.md` that describes the contents of each example folder. </p>
High-throughput crystallography for rapid early-stage fragment growth from crude arrays by low-cost robotics
<p>Data to support the paper - <em>High-throughput crystallography for rapid early-stage fragment growth from crude arrays by low-cost robotics</em>. Data includes a summary of X-ray and LCMS results for the reactions executed on the OpenTrons, output reports and summaries from MSCheck (semi-automated LCMS analyzer tool) and the Python scripts used to execute single and multistep chemistry on the OpenTrons.</p> <p><strong>Abstract</strong></p> <p>We demonstrate that a simple workflow of array synthesis, combining low-cost robotics with analytic techniques to deconvolute crude reaction mixtures, is an effective way to collect structural data on a binding site. Starting from the high information content of the crystallographic fragment screens on PHIP(2) (second bromodomain of the pleckstrin homology domain interacting protein), a collection of more than 1800 compounds was enumerated. Several thousand <em>Crude Reaction Mixtures</em> (CRMs) were synthesized on one robotic platform, an OpenTrons OT-1 liquid handler, using reaction sequences of up to 5 chemical steps. Analysis via MScheck, an algorithm-based system for finding a m/z in a CRM, significantly shortened product identification protocol times. 957 usable X-ray diffraction datasets were acquired, which resolved as 22 reaction products binding to the protein, 19 with conserved poses relative to the original fragment and 3 with a new, unexpected binding pose. The 22 crystallographic hit compounds were subsequently tested with peptide displacement alpha-screen assay and time-resolved grating-coupled interferometry-based biosensor assays, which confirmed one molecule with an IC<sub>50</sub> = 34 μM and K<sub>D</sub> = 50 μM, from an inactive fragment. The procedures described are entirely formulaic and engineerable and the method is eminently scalable. We anticipate that this cheap, low solvent-use approach will yield vast amounts of data, enabling rapid SAR landscape exploration around fragments, leading to faster fragment to lead times.</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.