Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data.
Accurate structural refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data was carried out using charge densities determined by the maximum-entropy method (MEM). The MEM charge density clearly revealed detailed features of the solvent region of the putative acylphosphatase crystalline structure, some of which had never been observed in conventional Fourier maps. The structural model in the solvent region was constructed as distributions of anisotropic water atoms. The omit-difference MEM maps and the difference MEM maps were effective in revealing details of the protein structure, such as multiple conformations of the side chains of amino-acid residues, anisotropy of atoms and H atoms. By model building using the MEM charge densities, the reliability factors R1 and R free in the SHELX refinement were dramatically improved from 17.9% and 18.3% to 9.6% and 10.0%, respectively. The present results prove the usefulness of MEM in improving the accuracy of refinement of protein crystal structures.
Nishibori
Eiji
E
Deparment of Applied Physics, Nagoya University, Nagoya 464-8603, Japan. eiji@mcr.nuap.nagoya-u.ac.jp
Nakamura
Takahiro
T
Arimoto
Masanori
M
Aoyagi
Shinobu
S
Ago
Hideo
H
Miyano
Masashi
M
Ebisuzaki
Toshikazu
T
Sakata
Makoto
M
D017766:Acid Anhydride Hydrolases / Q000737:chemistry*; D018360:Crystallography, X-Ray / Q000379:methods*; D019277:Entropy; D008958:Models, Molecular; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012984:Software; D014961:X-Ray Diffraction; D000097024:Acylphosphatase
D017766:Acid Anhydride Hydrolases; D000097024:Acylphosphatase