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Crystal structure of Blue Copper Oxidase from Nitrosomonas europaea
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 40% MPD, 4% Glycerol, pH 7.5, vapor diffusion, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.14 α = 81.48 b = 76.254 β = 73.38 c = 105.145 γ = 61.84
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-10-10 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 300 mm CCD 2008-10-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.91933 APS 21-ID-D 2 SYNCHROTRON APS BEAMLINE 23-ID-D 1.3811, 1.3189, 1.3476 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1,2 1.9 100.5 0.083 0.083 16.9 24.3 153165 23.92
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.9 1.97 98.2 0.342 0.342 4.8 2.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.9 48.28 153165 7696 97.74 0.168 0.166 0.1663 0.197 0.1967 RANDOM 23.915
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] -0.48 0.78 -0.38 -0.49 0.11 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_4_deg 21.423 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 6.188 r_scangle_it 2.206 r_scbond_it 1.39 r_angle_refined_deg 1.146 r_mcangle_it 0.84 r_mcbond_it 0.525 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_4_deg 21.423 r_dihedral_angle_3_deg 14.538 r_dihedral_angle_1_deg 6.188 r_scangle_it 2.206 r_scbond_it 1.39 r_angle_refined_deg 1.146 r_mcangle_it 0.84 r_mcbond_it 0.525 r_nbtor_refined 0.308 r_nbd_refined 0.183 r_symmetry_vdw_refined 0.136 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.084 r_metal_ion_refined 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15282 Nucleic Acid Atoms Solvent Atoms 1278 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction