Refinement at 1.4 Å resolution of a model of erabutoxin b: treatment of ordered solvent and discrete disorder

Abstract

The latter stages in the refinement of the protein erabutoxin b are described. The crystal structure of the 62-residue protein has been refined to a conventional R factor of 0.144 by stereochemically restrained least-squares methods using diffraction data to a limit of 1.4 A spacings. Emphasis was placed on determining as accurately as possible the solvent structure and the structures of heterogeneous groups in the protein. The final model includes two conformers for each of seven side chains and for an octapeptide segment. A total of 111 sites for water molecules have been located as well as one sulfate ion with a total of 68 site occupancies. 65 of the solvent sites overlap either with protein atoms belonging to groups in two alternative conformations or with other solvent sites. Dual protein conformers and overlapping solvent sites were both included in the least-squares refinement. Individual thermal and occupancy parameters were refined for solvent molecules. An analysis of these parameters has provided useful structural information.