Validation of nuclear magnetic resonance structures of proteins and nucleic acids: Hydrogen geometry and nomenclature

A statistical analysis is reported of 1,200 of the 1,404 nuclear magnetic r esonance (MMR)derived protein and nucleic acid structures deposited in the Protein Data Bank (PDB) before 1999. Excluded from this analysis were the e ntries not yet fully validated by the PDB and the more than 100 entries tha t contained < 95% of the expected hydrogens. The aim was to assess the geom etry of the hydrogens in the remaining structures and to provide a check on their nomenclature. Deviations in bond lengths, bond angles, improper dihe dral angles, and planarity with respect to estimated values were checked. M ore than 100 entries showed anomalous protonation states for some of their amino acids. Approximately 250,000 (1.7%) atom names differed from the cons ensus PDB nomenclature. Most of the inconsistencies are due to swapped proc hiral labeling. Large deviations from the expected geometry exist for a con siderable number of entries, many of which are average structures, The most common causes for these deviations seem to be poor minimization of average structures and an improper balance between force-field constraints for exp erimental and holonomic data. Some specific geometric outliers are related to the refinement programs used. A number of recommendations for biomolecul ar databases, modeling programs, and authors submitting biomolecular struct ures are given. Proteins 1999;37:404-416. (C) 1999 Wiley-Liss, Inc.