Improvement of protein phases by coarse model modification

A procedure is suggested for the refinement of a set of protein phases and for its extension to a higher resolution, which is a development of the approach of Agarwal & Isaacs [Proc. Natl Acad. Sci. USA, (1977), 74, 2835-2839]. A new set of phases is obtained by combining the starting phases with those calculated from a stereochemically non-conditioned coarse 'atomic' model which is automatically constructed and subjected to a least-squares refinement in reciprocal space. The method has been tested with actinidin data generated from atomic coordinates. Starting from the phases calculated to 3 Å resolution and the amplitudes calculated to 2 Å resolution a new set of phases was obtained with a mean error of 31° for 12 713 non-centrosymmetric reflections in the range to 2 Å. The refinement of the phases to 3 Å, resolution for γ-crystallin IIIb from calf lens and its extension to 2.7 Å resolution resulted in a noticeable improvement in the electron density map.