June 13, 2018 Dataset Open Access

Krojer, Tobias

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{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p><strong><a href=\"https://www.thesgc.org/scientists/groups/oxford\">SGC Oxford</a> has performed a crystallographic fragment screen on the human peroxisomal coenzyme A diphosphatase NUDT7 (<a href=\"http://www.uniprot.org/uniprot/P0C024\">UniProtKB - P0C024</a>). All structures with clearly identifiable ligands were deposited in the <a href=\"http://www.wwpdb.org/\">Protein Data Bank</a> under Group Deposition ID G_1002045. The final structures and the relevant PanDDA event maps can be found at the <a href=\"https://www.thesgc.org/fragment-screening\">SGC fragment screening website</a>. This work is part of the <a href=\"https://www.thesgc.org/tep\">Target Enabling Package (TEP)</a> program at SGC and the complete TEP for NUDT7 is will also be available on ZENODO shortly.</strong></p>\n\n<p>&nbsp;</p>\n\n<p><em><strong>Experiment</strong></em></p>\n\n<p>Crystals were prepared at the <a href=\"http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html\">XChem </a>facility of the <a href=\"http://www.diamond.ac.uk\">Diamond Light Source</a> (DLS). Briefly, crystals were soaked overnight with two fragment libraries; the Diamond- SGC Poised Library set (Cox et al., 2016) and the <a href=\"https://xchem.github.io/oxxchem/\">OxXChem</a> set with nominal fragment concentrations of 100 mM, with DMSO at 30% v/v. Additionally, a series of follow-up compounds based on an initial fragment hit was synthesized and soaked overnight with nominal compound concentrations of 30 mM, with DMSO at 30% v/v. All datasets were collected at <a href=\"http://www.diamond.ac.uk/Beamlines/Mx.html\">MX beamlines at DLS</a>. Autoprocessed datasets were analysed by Pan-Dataset Density Analysis (PanDDA) (Pearce et al., 2017). All ligands that were clearly identifiable in PanDDA event maps were modelled, refined and deposited into the PDB.</p>\n\n<p>&nbsp;</p>\n\n<p><em><strong>Content</strong></em></p>\n\n<p>This repository contains:</p>\n\n<ul>\n\t<li>all results from the PanDDA analysis, including ground-state-mean maps and PanDDA event &amp; Z-maps for all ligand bound structures</li>\n\t<li>MTZ and AIMLESS logfiles from auto-processing</li>\n\t<li>PDB, CIF &amp; PNG files of all the soaked compounds</li>\n\t<li>final refine.pdb and refine.mtz filess of all ligand bound structures</li>\n\t<li>all data belonging to an individual crystal can be found in <em>processed_datasets/&lt;crystal_ID&gt;</em></li>\n</ul>\n\n<p>&nbsp;</p>\n\n<p><em><strong>References</strong></em></p>\n\n<p>Cox, O. B. et al. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem. Sci. 7, 2322&ndash;2330 (2016).</p>\n\n<p>Pearce, N. M. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, (2017).</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Structural Genomics Consortium", 
      "@id": "https://orcid.org/0000-0003-0661-0814", 
      "@type": "Person", 
      "name": "Krojer, Tobias"
    }
  ], 
  "url": "https://zenodo.org/record/1244111", 
  "datePublished": "2018-06-13", 
  "keywords": [
    "PanDDA", 
    "Crystallographic Fragment Screening", 
    "Diamond Light Source beamline I04-1", 
    "XChem", 
    "Structural Genomics Consortium", 
    "Fragment Based Lead Discovery", 
    "NUDIX domain", 
    "NUDT7", 
    "Target Enabling Package (TEP)"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/4b8d2cfa-7ff0-453a-8249-77c1976ca5d6/panddas.2017-09-10.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
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  ], 
  "identifier": "https://doi.org/10.5281/zenodo.1244111", 
  "@id": "https://doi.org/10.5281/zenodo.1244111", 
  "@type": "Dataset", 
  "name": "PanDDA analysis of NUDT7 screened against DSPL and OxXChem fragment libraries"
}