C. Bystroff et al., PRISM - APPLICATION TO THE SOLUTION OF 2 PROTEIN STRUCTURES, Acta crystallographica. Section D, Biological crystallography, 49, 1993, pp. 440-448
The previous paper described a phase-refinement strategy for protein c
rystallography which exploited the information that proteins consist o
f connected linear chains of atoms. Here the method is applied to a mo
lecular-replacement problem, the structure of the protease inhibitor e
cotin bound to trypsin, and a single isomorphous replacement problem,
the structure of the N-terminal domain of apolipoprotein E. The starti
ng phases for the ecotin-trypsin complex were based on a partial model
(trypsin) containing 61 % of the atoms in the complex. Iterative skel
etonization gave better results than either solvent flattening or twof
old non-crystallographic symmetry averaging as measured by the reducti
on in the free R factor [Brunger (1992). Nature (London), 355, 472-474
]. Protection of the trypsin density during the course of the refineme
nt greatly improved the performance of both skeletonizing and solvent
flattening. In the case of apolipoprotein E, previous attempts using s
olvent flattening had failed to improve the SIR phases to the point of
obtaining an interpretable map. The combination of iterative skeleton
ization and solvent flattening decreased the phase error with respect
to the final refined structure, significantly more than solvent flatte
ning alone. The final maps generated by the skeletonization procedure
for both the ecotin-trypsin complex and apolipoprotein E were readily
interpretable.