ACCURACY AND PRECISION IN PROTEIN-STRUCTURE ANALYSIS - RESTRAINED LEAST-SQUARES REFINEMENT OF THE STRUCTURE OF POPLAR PLASTOCYANIN AT 1.33 ANGSTROM RESOLUTION

The structure of the electron-transfer protein, plastocyanin (99 amino acids, one Cu atom, 10 500 Da) from poplar leaves, has been refined at 1.33 angstrom resolution to a residual R = 0.15. The space group is orthorhombic, P2(1)2(1)2(1), a = 29.60 (1), b = 46.86 (3), c = 57.60 (3) angstrom. The 14 303 reflections used in the refinement were obtained from a data set recorded on a four-circle diffractometer with radiation from a sealed fine-focus tube, combined with a data set measured on oscillation films exposed at the DESY synchrotron. The final model comprises 1442 (738 non-H) protein atoms, one Cu atom and 110 solvent molecules. Nine residues are described as disordered. The root-mean-square deviation from ideal bond lengths is 0.016 angstrom and the root-mean-square difference between the positions of the C(alpha) atoms in this refined model and in the structure previously refined at 1.6 angstrom resolution is 0.11 angstrom. The effects of manual model adjustment, resolution, choice of standard values for geometrical parameters, inclusion of H atoms and inclusion of anomalous-scattering corrections on the copper-site geometry have been explored. The final values of the Cu-ligand bond lengths are: Cu-N(His37) 1.91, Cu-S(Cys84) 2.07, Cu-N(His87) 2.06, Cu-S(Met92) 2.82 angstrom.