Hierarchical normal mode refinement of anisotropic thermal parameters for supramolecular complexes

Abstract

In this thesis, we report a novel normal-mode based protocol for modeling anisotropic thermal motions of supramolecular complexes in x-ray crystallographic refinement, named HNMRef. The method models not only the global movements of the whole complex but also the deformational patterns of substructures. Compared with another widely adopted anisotropic thermal parameters refinement method—multi-group TLS, HNMRef delivers much more accurate thermal parameters for the complex and greatly simplifies the choice of substructure partition schemes. The effectiveness of the procedure is demonstrated on the refinements of a set of complexes with moderate resolutions. This protocol was shown to be able to significantly reduce the Rfree values of and improve the electron density maps. Moreover, the distribution of anisotropic thermal ellipsoids was much more consistent throughout the whole structure and agreed with the functional structure movements. We expect this protocol to be very effective in the anisotropic refinements of very large and flexible complexes with low or moderate-resolution x-ray diffraction data.