Large-scale comparison between the diffraction-component precision indexes favors Cruickshank’s Rfree function

Abstract

This study aims to provide a first large-scale comparison between the various diffraction-component precision index (DPI) equations, assess the applicability of the parameter, and make recommendations on DPI computation. The DPI estimates the average accuracy of atomic coordinates obtained by the structural refinement of protein diffraction data, with application in crystallography and cheminformatics. Although, Cruickshank and Blow proposed DPI equations based on R- and Rfree to calculate DPI values, these remain scarcely employed in the quality assessment of Protein Data Base (PDB) files, due to unclear data extraction protocols (to assign variables), complex equations, lack of extensive applicability studies and limited access to automated computations. In order to address these shortcomings, the entire RCSB PDB database was evaluated using Cruickshank's and Blow's R and Rfree DPI variations. Computations of 143070 X-ray structures indicate that Rfree-based DPI equations apply to 30 % more protein structures compared to R-based DPI equations, with Cruickshank Rfree-based DPI (CRF) exceeding the number of successful Blow?s Rfree-based DPI (BRF) computations. Although our results indicate that, in general, resolutions < 2 ? assure consistency among the various DPIs computations (differences <0.05 ?), we recommend the use of CRF DPI because of its wider applicability.