The application of direct methods and Patterson interpretation to high-resolution native protein data

Conventional small-molecule methods of solving the phase problem from native data alone, without the use of heavy-atom derivatives, known fragment geometries or anomalous dispersion, have been tested on 0.9 A resolution data for two small proteins: rubredoxin, from Desulfovibrio vulgaris, and crambin. The presence of three disulfide bridges in crambin and an FeS(4) unit in rubredoxin enabled automated Patterson interpretation as well as direct methods to be tried. Although both structures were already well established, the known structures were not used in the phasing attempts, except for identifying successful solutions. Direct methods were not successful for crambin, although the correct phases were stable to phase refinement and gave figures of merit clearly superior to any obtained in the ca 500 000 random starting phase sets that were refined. It appears that the presence of an iron atom in rubredoxin reduces the scale of the search problem by many orders of magnitude, but at the cost of producing 'over-consistent' phase sets that overemphasize the iron atom and involve partial loss of enantiomorph information. However, about 1% of direct-methods trials were successful for rubredoxin, giving mean phase errors of about 56 degrees (for all E > 1.2) that could be reduced to about 20 degrees by standard E-Fourier recycling methods. Limiting the resolution of the data degraded the quality of the solutions and suggested that the limiting resolution for routine direct-methods solution of rubredoxin is about 1.2 A. With the 0.9 A data, automated Patterson interpretation convincingly finds the three disulfide bridges in crambin and the FeS(4) unit in rubredoxin, and in both cases E-Fourier recycling starting from these 'heavier' atoms yields almost the complete structure. Whereas crambin could only be solved in this way at very high resolution, rubredoxin could be solved by Patterson interpretation down to 1.6 A. These results emphasize the benefits of collecting protein data to the highest possible resolution, and indicate that when a few 'heavier' atoms are present, it may prove possible in favorable cases to solve the phase problem from a single native data set collected to 'atomic resolution'.