The Accuracy of NMR Protein Structures in the Protein Data Bank

Abstract

The program ANSURR measures the accuracy of NMR structures, by comparing rigidity obtained from experimental backbone chemical shifts, and from structures. We report ANSURR analysis of NMR ensembles within the Protein Data Bank (PDB). NMR structures have improved in accuracy up till about 2005, since when accuracy has been fairly constant. Most structures have accurate secondary structure, but are generally too floppy, particularly in loops. There is a need for more experimental restraints in loops. The best current measures of accuracy are Ramachandran distribution and the number of NOE restraints per residue. The precision of structures within the ensemble correlates fairly well with accuracy, as does the number of hydrogen bond restraints per residue. If a structure contains additional components (such as additional polypeptide chains or ligands), then inclusion of these improves the accuracy of the structure. Analysis of over 7000 PDB NMR ensembles is available via our website ansurr.com.