Comparison of homology models with the experimental structure of a novel serine protease

A model structure of the human complement enzyme factor D was built based on homology with related serine proteases. A molecular-replacement solution of the factor D crystal structure employing the homology model refined without manual intervention to an R factor of 0.249 with 2.4 A native diffraction data. A multiple isomorphous replacement (MIR) electron-density map was subsequently produced, leading to a model refined at 2.0 A resolution to an R factor of 0.188. A homology model built with commercial modeling software was subjected to the same procedure. Comparisons of the homology models with the final refined MIR structure are presented. Major discrepancies were found in critical active-site regions.