THERMAL MOTION AND CONFORMATIONAL DISORDER IN PROTEIN CRYSTAL-STRUCTURES - COMPARISON OF MULTI-CONFORMER AND TIME-AVERAGING MODELS

Models describing thermal motion and conformational variability in pro tein crystal structures were applied to the refinement of a 1.8 angstr om crystal structure of penicillopepsin. Three methods were tested: co nventional refinement using restrained B factors, multiple-conformer r efinement, and time-averaging refinement using molecular dynamics. The information content of the models was assessed by cross-validation an d by estimating the phase accuracy of the model using phases obtained by multiple isomorphous replacement. The R value always decreased when using multi-conformer and time-averaging methods, as compared to conv entional refinement. In contrast, the cross-validated (''free'') R val ue and the phase accuracy worsened for time-averaging in vacuum. Inclu sion of solvent produced a slight improvement of both measures compare d to conventional refinement. Multi-conformer refinements always impro ved both measures. An optimum was reached for simultaneous refinement of between four and eight conformers. At the resolution limit of the p enicillopepsin data, multi-conformer refinement is an efficient method to describe conformational variability and thermal motion.