Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network

Abstract

Eight protein crystal structures, which have been refined against X-ray diffraction data extending to atomic resolution, 1.2 A or better, were inspected using four different validation tools, PROCHECK, PROVE, SQUID and WHATCHECK. Two general questions were addressed. (1) Do the structures imply changes in "expected" stereochemical properties and are the target values used for restraints in the validation programs and the refinement protocol appropriate? (2) Can errors in models be detected and how reliable are the coordinates after refinement? Preliminary analysis by members of the network led to modifications both to the validation programs and to the refinement protocols. The results of the final analyses are reported here. Apparent discrepancies in cell dimensions were identified. Most stereochemical properties are shown to be more tightly clustered than for lower resolution analyses. In contrast the omega angle has a wider distribution. The validation software is generally available and can be accessed at servers listed at the end of the paper.