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 fr agment geometries or anomalous dispersion, have been tested on 0.9 ang strom resolution data for two small proteins: rubredoxin, from Desulfo vibrio vulgaris, and crambin. The presence of three disulfide bridges in crambin and an FeS4 unit in rubredoxin enabled automated Patterson interpretation as well as direct methods to be tried. Although both st ructures were already well established, the known structures were not used in the phasing attempts, except for identifying successful soluti ons. Direct methods were not successful for crambin, although the corr ect phases were stable to phase refinement and gave figures of merit c learly superior to any obtained in the ca 500 000 random starting phas e 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 set s that overemphasize the iron atom and involve partial loss of enantio morph information. However, about 1% of direct-methods trials were suc cessful 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 degr aded die quality of the solutions and suggested that the limiting. res olution for routine direct-methods solution of rubredoxin is about 1.2 angstrom. with the 0.9 angstrom data, automated Patterson interpretat ion convincingly finds the three disulfide bridges in crambin and the FeS4 unit in rubredoxin, and in both cases E-Fourier recycling startin g from these 'heavier' atoms yields almost the complete structure. Whe reas crambin could only be solved in this way at very high resolution, rubredoxin could be solved by Patterson interpretation down to 1.6 an gstrom. These results emphasize the benefits of collecting protein dat a to the highest possible resolution, and indicate that when a few 'he avier' atoms are present, it may prove possible in favorable cases to solve the phase problem from a single native data set collected to 'at omic resolution'.