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The Uppsala Electron-Density Server.

Gerard J Kleywegt1, Mark R Harris, Jin Yu Zou

  • 1Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden. gerard@xray.bmc.uu.se

Acta Crystallographica. Section D, Biological Crystallography
|December 2, 2004
PubMed
Summary
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The Uppsala Electron Density Server (EDS) offers electron-density maps for 87% of crystallographic Protein Data Bank (PDB) entries. This resource details map generation methods and discusses associated challenges and project outcomes.

Area of Science:

  • Structural Biology
  • Crystallography
  • Bioinformatics

Background:

  • The Protein Data Bank (PDB) is a crucial repository for macromolecular structure data.
  • Electron-density maps are essential for interpreting and validating crystal structures.
  • Access to reliable electron-density maps and associated statistics is vital for researchers.

Purpose of the Study:

  • To describe the methods used to generate data for the Uppsala Electron Density Server (EDS).
  • To provide access to electron-density maps and structural fit statistics for a large subset of PDB entries.
  • To discuss challenges encountered during map generation and potential project spin-offs.

Main Methods:

  • Automated calculation of electron-density maps from deposited structure factors.

Related Experiment Videos

  • Validation of map quality by comparing calculated R values with published values.
  • Web-based dissemination of maps and statistics via the Uppsala Electron Density Server (EDS).

    • Main Results:

    • Electron-density maps are available for approximately 87% of eligible PDB entries.
    • The server provides statistics on the fit of crystal structures to their electron-density maps.
    • Successful reproduction of published R values within a five-percentage-point tolerance was a key criterion for map availability.

    Conclusions:

    • The Uppsala Electron Density Server (EDS) significantly enhances access to critical crystallographic data.
    • The server facilitates structure validation and interpretation for the broader scientific community.
    • Ongoing development and discussion of challenges continue to refine the map generation process.