Least-squares phase refinement. II. High-resolution phasing of a small protein

A recently described technique for direct least-squares refinement of phases has been successfully applied to the problem of phasing a 1.5 Å data set of observed structure-factor magnitudes for C. pasteurianum rubredoxin (M.W. ≃ 6100), given as a starting point a set of phases to 2.5 Å resolution as determined from heavy-atom derivatives. The result is a 1.5 Å X-ray structure for rubredoxin which generally confirms that recently obtained by a method involving the production and refinement of an approximate atomic model of the protein. In the present work the structure was obtained without chemical assumptions and with a considerable saving of effort compared with the previous determination. The technique also avoided certain small errors in the assignment of side-group structures made in the previous determination. Final high-resolution phasing would result from conventional refinement of the direct-method structure. An additional point of interest is that the structure of a protein at the atomic level, elucidated on purely physical principles, has been found to agree with the deductions from chemistry.