Ab initio structure determination of cytochrome c6 by combined reciprocal space-real space approach

Abstract

Abstract The direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c6, a heme-containing redox protein with 89 amino acids, a Fe atom and 151 solvent water molecules in the asymmetric unit and data to 1.1 Å resolution. The crystal system is rhombohedral with space group R3, cell parameters a = b = c = 40.43(10) Å, α = β = γ = 80.25(5)°. Starting with initially random phases, useful phase sets could be obtained from multiple trials of direct methods based on reciprocal space. The E-map corresponding to the phase set with the lowest mean phase error, 45.4°, showed a distorted octahedral coordination around the Fe site. The phase estimates from the metal atom and a few neighbouring atoms in the initial E-map have been improved by density modification procedure (PERP) operating in direct space. The resulting electron density map can be interpreted readily by an automated procedure to build up the protein structure.