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X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NDT PDB ENTRY 1NDT MONOMER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 30% PEG 4K, 0.1M MAGNESIUM CHLORIDE, 0.1M TRIS-HCL PH8.5, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.87 56.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.106 α = 90 b = 106.106 β = 90 c = 63.647 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE FUJI TORROIDAL MIRROR 1999-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A Photon Factory BL-6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.9 52.705 93.1 0.067 6.1 4.5 29659 15.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 83.4 0.331 2.2 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NDT MONOMER 1.9 20 28145 1488 91.2 0.172 0.171 0.199 RANDOM 25.78
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 28 p_staggered_tor 13.1 p_planar_tor 4.7 p_scangle_it 2.487 p_mcangle_it 1.987 p_scbond_it 1.619 p_mcbond_it 1.306 p_multtor_nbd 0.238 p_singtor_nbd 0.173 p_xyhbond_nbd 0.119
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 28 p_staggered_tor 13.1 p_planar_tor 4.7 p_scangle_it 2.487 p_mcangle_it 1.987 p_scbond_it 1.619 p_mcbond_it 1.306 p_multtor_nbd 0.238 p_singtor_nbd 0.173 p_xyhbond_nbd 0.119 p_plane_restr 0.03 p_angle_d 0.029 p_bond_d 0.011 p_angle_deg p_planar_d p_hb_or_metal_coord p_chiral_restr p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2575 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction CCP4 data scaling AMoRE phasing