Quality assessment of NMR structures: a statistical survey.
A statistical analysis is reported of experimental data and coordinates of a set of 97 NMR structures deposited in the PDB. The aim is to assess the quality of these structures in relation to the amount of experimental information. Experimental restraints were analysed using the program AQUA. Many nomenclature inconsistencies between deposited restraint and coordinate files were observed. The experimental restraint files were found to contain a high proportion of redundant restraints. Procedures for analysing and correcting the inconsistencies and restraint counts are described. The analysis of NOE restraint violations (using AQUA) and of a wide variety of geometrical quality indicators (using PROCHECK-NMR and WHAT IF) provides a reference for other NMR structure determinations. The extent of NOE violations is anti-correlated with the quality of the Ramachandran map. The precision as measured by the circular variance of backbone dihedral angles, does increase with the amount of experimental data, as expected, but is sometimes overestimated. Bond lengths, bond angles and planarity of groups can deviate considerably from ideal values. Outliers appear to cluster per laboratory, indicating that the results depend on particulars of refinement protocols and/or software. We have identified a problem of atom overlap in a number of refined structures.We recommend adhering to the standard nomenclature as put forward by an IUPAC Task Group, to ensure consistency between restraints and coordinates, and to omit redundant restraints from the deposition. The results obtained from this analysis and the AQUA program are available through the World Wide Web.
Doreleijers
J F
JF
Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands.
Rullmann
J A
JA
Kaptein
R
R
D016208:Databases, Factual; D009682:Magnetic Resonance Spectroscopy; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D011786:Quality Control; D012984:Software; D009626:Terminology as Topic
D011506:Proteins