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Annealed structure of oxidized bovine cytochrome c oxidase with reduced metal centers induced by synchrotron X-ray exposure
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 4.07 69.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.037 α = 90 b = 182.633 β = 90 c = 205.453 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 2019-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9790 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.45 40 99.85 0.993 6.9 6.9 244470
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 99.9 0.402 0.9
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 2.45 39.303 244470 12054 99.851 0.209 0.2063 0.215 0.253 0.2589 46.829
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] -3.551 -1.654 5.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.253 r_dihedral_angle_3_deg 17.352 r_dihedral_angle_4_deg 16.426 r_lrange_it 8.711 r_lrange_other 8.711 r_dihedral_angle_1_deg 6.977 r_scangle_it 6.296 r_scangle_other 6.296 r_mcangle_it 5.165 r_mcangle_other 5.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.253 r_dihedral_angle_3_deg 17.352 r_dihedral_angle_4_deg 16.426 r_lrange_it 8.711 r_lrange_other 8.711 r_dihedral_angle_1_deg 6.977 r_scangle_it 6.296 r_scangle_other 6.296 r_mcangle_it 5.165 r_mcangle_other 5.165 r_dihedral_angle_other_3_deg 4.395 r_scbond_it 3.95 r_scbond_other 3.95 r_mcbond_it 3.303 r_mcbond_other 3.303 r_chiral_restr_other 2.047 r_angle_refined_deg 1.622 r_angle_other_deg 1.262 r_symmetry_nbd_refined 0.228 r_nbd_refined 0.215 r_nbd_other 0.212 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.162 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28488 Nucleic Acid Atoms Solvent Atoms 914 Heterogen Atoms 2276
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing