REFINEMENT STRATEGIES FOR PROTEIN-NUCLEIC ACID COMPLEXES. G. N. Parkinson, B. Schneider, J. Vojtechovsky, R. H. Ebright, and H. M. Berman, Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855.

Protein-DNA complex crystals offer an obvious path towards visualizing modes of recognition, stabilization, interaction, and conformation of nucleic acids and proteins. We are studying a series of such crystalline complexes containing Catabolite Activating Protein (CAP) and DNA with particular emphasis on understanding the detailed interactions between the amino acid side chains and the nucleic acid bases. To do this, it is necessary to exercise special care with the refinement process.

In order to achieve improved results, we created a nucleic acid parameter file (Parkinson, et al., Acta Cryst. D52, 57 1996) for use with X-PLOR that incorporated newly determined standard values for the bond distances, bond angles, and dihedral angles. More recently we have expanded the parameter file to include dihedrals for three DNA conformational classes.

The strategies for refinement of these complexes that allow for the correct balance between the macromolecular components will be discussed.

Supported by grants from NIH (GM 21589) and NSF (BIR 9305135).