Improved low-resolution crystallographic refinement with Phenix and Rosetta

Abstract

Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to converge on a structure with realistic geometry. We developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray refinement in Phenix. On a set of difficult low-resolution cases, the method yielded improved model geometry and lower free R factors than alternate refinement methods.While determination of X-ray crystal structures at moderate to high resolutions has recently accelerated, structure determination and refinement at lower resolutions remains problematic 1 despite considerable recent work 2-8 . We reasoned that combining the strengths of the Rosetta structure modeling methodology and the Phenix X-ray refinement software could yield improved refinement at low resolution. Rosetta utilizes a detailed all-atom force field that could partially compensate for the lack of high-resolution data, as well as search procedures combining backbone minimization with discrete side-chain optimization that more effectively explore alternative side-chain arrangements than does simulated annealing. Phenix is a state-of-the-art X-ray refinement package that can be readily integrated with