A direct-method ab initio phasing of a protein, cupredoxin amicyanin, at 1.31 A resolution

The direct-methods program MULTAN88 has been applied successfully to redetermine the structure of a protein, cupredoxin amicyanin, containing 808 non-H atom sites, one Cu atom and 132 ordered water molecules in the asymmetric unit using data at 1.31 A resolution. Starting with initially random phases, useful phase sets selected by figures of merit could be obtained from multiple trials. The E maps corresponding to the best eight phase sets in order of combined figures of merit (CFOM2) revealed a distorted tetrahedral geometry around the Cu site. The phase estimates from the metal and a few neighbouring atoms in the initial E map corresponding to the set with the highest CFOM2 could be improved by the density-modification procedure PERP and led to an interpretable electron-density map.