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Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Manual refineme ...
Crystal structures were rigid-body fit into the density map and model optimization was then carried out with Phenix real-space refine. Manual refinement in Coot was performed to ensure that the backbone traces followed the density in regions where the map was high enough resolution to trace the backbone. Secondary structure restraints were used to ensure that alpha-helices and beta-sheets did not deviate far from their expected geometry. A final check of MolProbity and cross correlation was done to ensure model quality.