Protein crystallography : new approaches to X-ray data collection, direct space refinement and model building

Abstract

This crystallographic study was designed to develop and test efficient techniques of X-ray data collection, phase extension and refinement, and model building capable of giving a reliable description of macromolecules in particular the extracellular nuclease of Staphylococcus aureus. Since protein crystals are irreparably damaged upon exposure to X-radiation, the data collection procedure minimized radiation damage by measuring first only the raw peak intensities using limited oi step scans and by sampling the background levels subsequent to all peak intensities. In testing the limited three step w scanning technique on a small molecular complex, the w scanning procedure gave the same refined model as the standard 0/2θ scanning method. In order that the peak intensity data could be measured with a minimal amount of radiation damage, a background collection procedure was developed which would sample the backgrounds of the entire range of data subsequent to peak data collection. Using Fourier interpolation and smoothing techniques, the sampled background was manipulated to give reliable estimates of the individual backgrounds. The combination of these two procedures allowed the collection of a complete 1.5A data set for the pdTp inhibited form of nuclease. To obtain higher resolution maps than that afforded by isomorphous replacement techniques, a direct space refinement procedure developed by Collins (1975) was tested on the protein rubredoxin and was used to refine and extend the phasing for nuclease. In both cases the direct space refined map was significantly improved over the initial map phased by isomorphous replacement methods..