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Quality assessment of NMR structures: a statistical survey
J F Doreleijers1, J A Rullmann, R Kaptein
1Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
Journal of Molecular Biology
|July 29, 1998
Summary
This study analyzed 97 NMR structures, finding inconsistencies and redundant restraints in deposited data. Recommendations are provided for improving the quality and consistency of Nuclear Magnetic Resonance structure determination.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Nuclear Magnetic Resonance (NMR) structure determination is crucial for understanding biomolecular function.
- The Protein Data Bank (PDB) archives experimentally determined structures, including those from NMR.
- Assessing the quality of deposited NMR structures is essential for reliable scientific interpretation.
Purpose of the Study:
- To statistically analyze the quality of 97 NMR structures deposited in the PDB.
- To evaluate the relationship between experimental data quantity and structural quality.
- To identify common issues in NMR structure determination and deposition.
Main Methods:
- Analysis of experimental data and coordinates from 97 PDB-deposited NMR structures.
- Utilized AQUA program for analyzing experimental restraints and NOE restraint violations.
- Employed PROCHECK-NMR and WHAT IF for assessing geometrical quality indicators.
Main Results:
- Observed significant nomenclature inconsistencies between restraint and coordinate files.
- Identified a high proportion of redundant restraints in experimental restraint files.
- Found anti-correlation between NOE restraint violations and Ramachandran map quality; precision can be overestimated; outliers cluster by laboratory; atom overlap issues noted.
Conclusions:
- Adherence to standard nomenclature and omission of redundant restraints are recommended for consistency.
- NMR structure quality is influenced by refinement protocols and software.
- The study provides a reference for evaluating NMR structure quality and identifies areas for improvement in data deposition.