NEW PARAMETERS FOR THE REFINEMENT OF NUCLEIC ACID-CONTAINING STRUCTURES

Structures at atomic resolution (up to 1.0 Angstrom) which contain bas es, sugars or the phosphodiester linkage, were selected from the Nucle ic Acid Database or the Cambridge Structural Database to build a nucle ic acid dictionary from X-ray refined structures. The dictionary consi sts of the average values for bond distances, bond angles and dihedral angles. The variance of the sample is used to provide information abo ut the expected r.m.s. deviations of the refined parameters. A diction ary was constructed for refinement trials in X-PLOR. The dictionary in cludes RNA and DNA in C2'-endo and C3'-endo sugar pucker conformations , as well as values for the backbone dihedrals. Tests were performed o n the dictionary using three structures: a B-DNA, a Z-DNA and a protei n-DNA complex. During the course of refinement, all three structures s howed significant improvements as measured by r.m.s. deviations and R factors when compared to the previous DNA dictionary.