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DCC: a Swiss army knife for structure factor analysis and validation.

Huanwang Yang1, Ezra Peisach1, John D Westbrook1

  • 1Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Chemistry and Chemical Biology, Center for Integrative Proteomics Research, Rutgers, State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA.

Journal of Applied Crystallography
|June 9, 2016
PubMed
Summary
This summary is machine-generated.

The Data Comparison and Construction (DCC) program validates X-ray crystallography models against experimental data. This tool enhances the accuracy and reliability of structural data archived in the Protein Data Bank.

Keywords:
DCCProtein Data Bankstructure factor validationutility programs

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Since 2008, the Protein Data Bank (PDB) mandates the submission of experimental structure factor data for X-ray structure depositions.
  • Ensuring the quality and consistency of deposited structural data is crucial for scientific reproducibility.

Purpose of the Study:

  • To introduce the Data Comparison and Construction (DCC) program developed by RCSB PDB.
  • To streamline the validation of X-ray crystallographic models against experimental data for biocurators.

Main Methods:

  • The DCC program is a command-line tool that integrates multiple third-party software packages.
  • It performs structure factor validation, electron density map generation and analysis, and residual B factor analysis.
  • The program facilitates comparison between structural models and experimental data.

Main Results:

  • DCC enables biocurators to efficiently validate structural models against experimental data.
  • It provides comprehensive crystallographic statistics in PDBx/mmCIF format.
  • The output is suitable for automated data processing and archiving.

Conclusions:

  • The DCC program standardizes and automates the validation process for X-ray structure depositions.
  • It enhances the quality control of data submitted to the Protein Data Bank.
  • DCC supports the integrity and accessibility of structural biology data.