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Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source
Published on: May 29, 2021
Re-refinement from deposited X-ray data can deliver improved models for most PDB entries
Robbie P Joosten1, Thomas Womack, Gert Vriend
1CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
Acta Crystallographica. Section D, Biological Crystallography
|January 28, 2009
Summary
Automated X-ray structure refinement improves Protein Data Bank (PDB) entries by incorporating new methods. Combining automated refinement with validation and analysis helps identify and fix structural problems, enhancing data quality.
Area of Science:
- Structural Biology
- Biophysics
- Computational Biology
Background:
- Protein Data Bank (PDB) entries are structural models derived from X-ray crystallography data.
- Advances in X-ray crystallography methods necessitate re-evaluating and improving existing structural models.
- Current automated refinement protocols often require manual intervention to address validation issues.
Purpose of the Study:
- To develop an improved automated re-refinement protocol for PDB entries.
- To identify and catalogue problems in PDB entries that can be automatically corrected.
- To assess the effectiveness of automated re-refinement in improving structural models.
Main Methods:
- Automated gradient refinement protocols applied to PDB entries.
- Integration of structure validation software and difference-density peak analysis.
- Systematic use of the TLS (Translation/Libration/Screw) parameterization for B-factors.
Main Results:
- Automated re-refinement successfully improved PDB entries, including recent high-resolution structures.
- Improvements were often linked to the systematic application of TLS parameterization.
- Manual and semi-manual map analysis and fitting steps showed potential for future automation.
Conclusions:
- Automated re-refinement, combined with validation and analysis, enhances PDB data quality.
- TLS parameterization is a key factor in achieving structural improvements.
- Expanding deposition scope to include refinement metadata and primary X-ray data could further advance re-refinement.
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