Figure 2.

Method comparison. (A) Histogram of R_free values after autobuilding for the seven difficult blind cases solved using the new approach (Table 1, set B). For most existing approaches, none of the cases yielded R_free values under 50%; DEN was able to reduce R_free to 45–49% for three of the structures. For all seven cases, Rosetta energy and density guided structure optimization led to R_free values under 40%. (B) Dependence of success on sequence identity. The fraction of cases solved (R_free after Autobuilding < 40%) is shown as a function of template sequence identity over the 18 blind cases and 59 benchmark cases. The new method is a clear improvement below 28% sequence identity. (C) Dependence of structure determination success on initial map quality. Sigma-A weighted 2mFo-DFc density maps (contoured at 1.5σ) computed from benchmark set templates with divergence from the native structure increasing from left to right are shown in grey; the solved crystal structure is shown in yellow. The correlation with the native density is shown above each panel. The solid green bar indicates structures the new approach was able to solve (R_free<0.4); the red bar those that torsion-space refinement or DEN refinement is able to solve, and the purple bar those that can be solved directly using the template.