An evaluation of the use of databases in protein structure refinement

The speed of electron-density fitting during X-ray structure solution and refinement, and the quality of the protein model resulting, can both be enhanced by the use of databases of main- and side-chain conformations. Three structures are compared in this report, one refined at high resolution (1.7 A), and two at lower resolutions using either the database method (2.4 A resolution) or more traditional empirical electron-density fitting (1.9 A resolution). An analysis of peptide orientation was used as an aid in finding unusual portions of main-chain structure. The fit of side chains to known rotamer conformations was used to help determine the accuracy of these atomic positions. In addition, the use of an objective measure of the fit of structures to electron-density maps was evaluated, both alone and in combination with side-chain conformational information.