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Structure of oxidized bovine cytochrome c oxidase at 1.90 Angstrom resolution obtained by synchrotron X-rays
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 PEG 4000, Potassium phosphate, Decylmaltoside
Crystal Properties Matthews coefficient Solvent content 4.13 70.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.118 α = 90 b = 182.415 β = 90 c = 208.547 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 40 99.9 0.139 0.996 7.8 6.9 528165
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 2.105 0.442
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DYR 1.9 39.989 528021 26755 99.833 0.186 0.1846 0.1958 0.2152 0.2249 43.502
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] -2.807 -0.347 3.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.631 r_dihedral_angle_4_deg 16.843 r_dihedral_angle_3_deg 15.564 r_lrange_it 8.638 r_lrange_other 8.638 r_scangle_it 6.975 r_scangle_other 6.975 r_dihedral_angle_1_deg 6.631 r_mcangle_it 4.876 r_mcangle_other 4.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.631 r_dihedral_angle_4_deg 16.843 r_dihedral_angle_3_deg 15.564 r_lrange_it 8.638 r_lrange_other 8.638 r_scangle_it 6.975 r_scangle_other 6.975 r_dihedral_angle_1_deg 6.631 r_mcangle_it 4.876 r_mcangle_other 4.876 r_scbond_it 4.843 r_scbond_other 4.843 r_mcbond_it 3.556 r_mcbond_other 3.556 r_dihedral_angle_other_3_deg 2.257 r_chiral_restr_other 2.066 r_angle_refined_deg 1.767 r_angle_other_deg 1.403 r_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.179 r_nbd_other 0.176 r_symmetry_nbd_refined 0.175 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.049 r_xyhbond_nbd_other 0.021 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28488 Nucleic Acid Atoms Solvent Atoms 1693 Heterogen Atoms 2732
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing