Crystallographic structure refinement of Chromatium high potential iron protein at two Angstroms resolution.

The structure of Chromatium high potential iron protein (HiPIP) has been refined by semiautomatic Fo-Fc (observed minus calculated structure amplitude Fourier methods to a convential R index, R=sum of the absolute value of Fo-Fc divided by the sum of Fo, of 24.7% for a model in which bond distances and angles are constrained to standard values. Bond length and angle constraints were applied only intermittenly during the computations. At a late stage of the refinement, atomic parameters for only the Fe4S4 cluster plus the 4 associated cystein S-gamma atoms were adjusted by least squares methods and kept fixed during the rest of the refinement. The refined model consists of 625 of the 632 nonhydrogen atoms in the protein plus 75 water molecules. Seven side chain atoms could not be located in the final electron density map. A computer program rather than visual inspection was used wherever possible in the refinement: for locating water molecules, for removing water molecules that too closely approach other atoms, for deleting atoms that lay in regions of low electron density, and for evaluating the progress of refinement. Fo-Fc Fourier refinement is sufficiently economical to be applied routinely in protein crystal structure determinations. The complete HiPIP refinement required approximately 12 hours of CDC 3600 computer time and cost less than $3000 starting from a "trial structure," based upon multipe isomorphoous replacement phases, which gave an R of 43%...