Potential use of real-space refinement in protein structure determination

Through testing refinement protocols using free R-factor estimates of model quality, it is shown that real-space refinement can be a useful addition to conventional reciprocal-space refinement, even for protein structures with poor electron-density maps derived from multiple isomorphous replacement. By alternating real- and reciprocal-space refinements, starting with an experimental map, then calculating 2F_o - F_c maps, it is demonstrated with the structure of HMG-CoA reductase, that quick automatic refinement can yield a model with a free R factor 1.5% better than exhaustive reciprocal-space refinement, and within 1% of a model that was interactively rebuilt and refined repeatedly.