Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

Abstract

The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 A, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.

Figure 1

Outline of AutoBuild wizard operation beginning from experimental phase information.

Figure 2

R factors (closed diamonds) and free R factors (open triangles) of final models obtained with the AutoBuild wizard for 48 structures from the PHENIX structure library beginning with experimental phases obtained with the AutoSol wizard. (a) R and free R factors as a function of resolution of the data used in modelling. (b) R and free R factors as a function of the correlation coefficient of the starting density-modified experimental map. (c) R factors as in (a), except that only structures with a correlation coefficient of the starting density-modified experimental map of greater than 0.85 are included.

Figure 3

Completeness of main-chain model (closed diamonds) and assignment of residues to sequence (open triangles) of final models in Fig. 2 ▶. (a) Completeness as a function of resolution of the data used in modelling. (b) Completeness as a function of the correlation coefficient of the starting density-modified experimental map to the model map. (c) Completeness as a function of resolution as in (a), except that only structures with a correlation coefficient of the starting density-modified experimental map of greater than 0.85 are included.

Figure 4

Main-chain (closed diamonds) and side-chain (open triangles) r.m.s.d. of final models in Fig. 2 ▶ compared with refined models previously obtained for the same structures. (a) R.m.s.d. as a function of resolution of the data used in modelling. (b) R.m.s.d. as a function of the correlation coefficient of the starting density-modified experimental map. (c) R.m.s.d. as in (a), except that only structures with a correlation coefficient of the starting density-modified experimental map of greater than 0.85 are included.