Dynamic structure of human lysozyme derived from X-ray crystallography: normal mode refinement.

X-ray crystallography provides a wealth of information about the dynamic as well as static protein structure. A new method of dynamic structure refinement of protein X-ray crystallography, normal mode refinement, is proposed. In this method, the Debye-Waller factor is expanded in terms of the low-frequency internal normal modes and external normal modes, whose amplitudes and couplings are optimized in the process of crystallographic refinement. The internal and external contributions to the atomic fluctuations can be separated. Also, anisotropic atomic fluctuations and their inter-atomic correlations can be determined experimentally even with a relatively small number of adjustable parameters. The method is applied to the analyses of experimental data of human lysozyme and its mutant, C77A/C95A, to reveal its dynamic structure.