Acta Cryst. (1992). B48, 42-59 Refinement of Rubredoxin from Desulfovibrio vulgaris at 1.0 ~ with and without Restraints

X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part syn-chrotron radiation and in part X-rays from a sealed-tube Mo Ka source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2 ~ with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and fl = 108.3. The overall merg-ing R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90 % of the pro-tein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model