VP40 Crystal soaking Data Repository, Institute for Virology, Becker Lab

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https://data.uni-marburg.de/handle/dataumr/253
This repository contains structural data (.mtz) of Sudan virus VP40 crystals, soaked with small molecules. For each fragment the crystal data set name(s) are listed, including the resolution, soaking times, PanDDA result as well as follow-up refinement notes (see "Overview of crystal soaking datasets").

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    Structural reflection data (.mtz) of soaked Sudan virus VP40 crystals
    (Philipps-Universität Marburg, Institut für Virologie) Werner, Anke-Dorothee; Becker, Stephan
    This repository contains structural data (.mtz) of Sudan virus VP40 crystals, soaked with small molecules. Files are ordered names correspond to internal lab crystal IDs (e.g. XDS_ASCII_AW61_scaled1.mtz, with "AWxxx" indicating the crystal ID). The resolution and data quality indicators for each dataset are provided in an accompanying metadata file. Users should refer to this file to select appropriate datasets for their analyses. Dimeric VP40 (approx. 7 mg/ml in 25 mM Tris, 300 mM NaCl, pH 8) was mixed 1:1 with crystallization buffer (100 mM HEPES, 40 mM MgCl2, 10% v/v PEG400). Crystals grew overnight at 18 °C using the hanging drop method. Fragments originating from the FragXtal Screen (Jena Biosciences) were dissolved in DMSO to 1 M and diluted 1:10 in crystallization buffer (with or without 20% ethylene glycol as a cryoprotectant) to a final concentration of 100 mM. Crystals were then placed in a drop of the diluted fragments and soaked for either only seconds, minutes, 1 h, or overnight. Crystals were then harvested, flash-frozen in liquid nitrogen and analyzed at the Swiss Light Source, Paul-Scherrer Institute, Villigen, Switzerland (SLS BEAMLINE X06SA, DECTRIS EIGER X 16M detector, single wavelength, data collection temperature 100 K). Datasets were collected and processed using XDS and scaled using the ccp4i suite Aimless. Mtz-files can be used for molecular replacement (using PDB-ID 8B3X or other structures of VP40 as template). To use these mtz files for molecular replacement: 1) Download the desired mtz file(s) and the accompanying metadata. 2) Initial Structure Solution: a. Use molecular replacement with programs such as Phaser or MOLREP from the CCP4 suite. b. Use PDB-ID 8B3X as the initial search model. Other VP40 structures may also be suitable. 3) Rapid Initial Model Building and Refinement: a. Use DIMPLE (Difference Map Pipeline) for quick initial refinement and map calculation. b. Run DIMPLE. c. This will produce refined models and maps for each dataset, suitable for initial analysis or as input for PanDDA. 4) Fragment Identification: a. For datasets suspected to contain bound fragments, use PanDDA (Pan-Dataset Density Analysis). b. Prepare input files as per PanDDA documentation, using DIMPLE output. c. Run PanDDA with appropriate parameters. d. Examine PanDDA event maps for evidence of bound fragments. 5) Model Building and Refinement: a. Build fragments into positive difference density or PanDDA event maps. b. Refine structures using programs like REFMAC5 or phenix.refine. Related datasets deposited to the Protein data bank (https://www.rcsb.org/) include 8B2U (Crystal structure of SUDV VP40 in complex with salicylic acid) and 8B1S (Co-crystal of SUDV VP40 with salicylic acid). This work was funded by the LOEWE Center DRUID (State of Hesse, Germany), project A1. For any questions regarding the use of these datasets or analysis methods, please contact the depositing authors Stephan Becker or Anke-Dorothee Werner at the insitutte for Virology, Marburg, Germany (https://www.uni-marburg.de/en/fb20/departments/ciii/virology).