X-ray refinement of protein structures by simulated annealing: test of the method on myohemerythrin

The recently developed method of structure factor refinement by molecular dynamics with simulated annealing [Brünger, Kuriyan & Karplus (1987). Science, 235, 458-460] is tested on the 118 residue protein myohemerythrin. A highly refined structure for this protein at 1.3/1.7 A resolution has recently been published [Sheriff, Hendrickson & Smith (1987). J. Mol. Biol. 197, 273-296]. This is compared with the results of simulated annealing refinement (with no manual intervention) starting from an earlier model for the protein from a stage in the refinement when conventional least-squares methods could not improve the structure. Simulated annealing reduces the R factor at 2.5 A from 39 to 31%, with uniform temperature factors and no solvent molecules and with similar stereochemistry; the comparable value for the manually refined structure is 27.9%. Errors in backbone and sidechain positions up to about 3 A are corrected by the method. The error in backbone positions for roughly 85% of the initial structure is within this range, and in these regions the r.m.s. backbone error is reduced from 1.1 to 0.4 A. For the rest of the structure, including a region which was incorrectly built due to a sequence error, the procedure does not yield any improvement and manual intervention appears to be required. Nevertheless, the overall improvement in the structure results in electron density maps that are easier to interpret and permit identification of the errors in the structure. The general utility of the simulated annealing methodology in X-ray refinement is discussed.