Anisotropic thermal-parameter refinement of the DNA dodecamer CGCGAATTCGCG by the segmented rigid-body method

Abstract

A structure-factor least-squares refinement of the deoxyoligonucleotide (CGCGAATTCGCG)2 has been conducted using a model with constraints and restraints on the positional parameters and a segmented rigid-body representation for the anisotropic temperature factors. The macromolecule was divided into subgroups each of which was treated as a rigid body in terms of both positional and thermal parameters. For each subgroup, the thermal parameters determined were elements of translation, libration and correlation (TLS) tensors. This segmented rigidbody model of thermal motion has not previously been applied to the refinement of a macromolecular crystal structure. The anisotropic thermal-parameter refinement has significantly reduced the classical R factor as judged by the Hamilton test. The resulting difference Fourier map has a considerably lower noise level allowing fifteen additional low-occupancy water positions to be identified. In addition, analysis of the anisotropic thermal parameters has revealed new information about the local mobility of the groups in the oligonucleotide. Thus, the method of segmented rigid-body anisotropic temperature-factor refinement appears to be uniquely suited to macromolecules, especially nucleic acids, where high-resolution data are usually unavailable.