Getting Better Information into and Out of High-Resolution Structures

Abstract

My research aims to aid some of the difficult but important parts of model building at very high resolution. Using ubiquitin as a test case, I am working to improve the modeling of alternate conformations both at room temperature and at cryogenic temperature. In addition, we hope to advance the modeling of ions, in particular the relationship of partial occupancy ions to alternate conformations. I currently have three high-resolution structures at cryo-temperature between 1.0A and 1.2A, and I have room-temperature structures between 1.3A and 1.5A. We are currently working to identify alternate networks for mutagenesis and further structural studies. By collecting high-resolution data in a variety of space groups and conditions, we hope to better understand the link between ubiquitin conformational variability and binding specificity.Another aspect of my project involves getting better information into high-resolution models. Our group has previously developed all-atom contact analysis and the MolProbity web service, and these features are now incorporated into the PHENIX crystallographic software system. However, our tools position hydrogens at the nucleus, but PHENIX places them at the centers of the electron clouds. Because the electron cloud is what diffracts X-rays and what matters in evaluating steric contacts, we are working to update parameters in both services. In conjunction with collaborators who are assessing the hydrogen bondlengths, my work uses a database-drive approach to evaluate our current van der Waals radii. Recalibrating the van der Waals radii is important because the radii directly influence contact analysis. We have now settled on a new set of bondlengths and radii and are working to implement these values in both PHENIX and MolProbity. Our new parameters will improve the validation tools available to the crystallographic community, thereby allowing our users to better detect model errors.