Phase extension and refinement by density modification in protein crystallography

A new procedure of phase extension and refinement via electron density modification applicable to low-resolution protein crystal structures is described. The Sperm Whale myoglobin structure has been used as a working molecule. The procedure of phase extension has firstly been tested starting from a set of calculated phases at 4 Å resolution; the mean phase error obtained for the 9000 strongest reflections from 4 to 1.8 Å was 39°; subsequently a mean phase error of 30° was spread into the low-resolution set and a phase refinement and extension procedure was carried out to 1.8 Å resolution. The final mean phase errors of the 1184 low-resolution model and of the 4816 strongest reflections within 1.8 Å were 22 and 50° respectively. The map calculated with this final set of reflections approaches in quality and details the map calculated with the 12 658 phases from the refined coordinates.