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Crystal structure of thiocyanate bound bovine cytochrome c oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 PEG4000, Potassium phosphate, Decylmaltoside
Crystal Properties Matthews coefficient Solvent content 4.19 70.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.316 α = 90 b = 185.058 β = 90 c = 208.477 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 2022-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 2.06641 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 2.388 138.398 95.6 0.138 0.998 14.7 13.1 178585
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 2.388 2.666 1.405 0.665
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.388 30.002 178421 8964 65.608 0.19 0.1869 0.1929 0.2418 0.2423 52.314
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] 0.353 -0.823 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.941 r_dihedral_angle_4_deg 18.762 r_dihedral_angle_3_deg 16.857 r_lrange_it 10.838 r_lrange_other 10.838 r_dihedral_angle_1_deg 7.04 r_scangle_it 6.723 r_scangle_other 6.723 r_dihedral_angle_other_3_deg 6.436 r_mcangle_it 5.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.941 r_dihedral_angle_4_deg 18.762 r_dihedral_angle_3_deg 16.857 r_lrange_it 10.838 r_lrange_other 10.838 r_dihedral_angle_1_deg 7.04 r_scangle_it 6.723 r_scangle_other 6.723 r_dihedral_angle_other_3_deg 6.436 r_mcangle_it 5.697 r_mcangle_other 5.697 r_scbond_it 4.229 r_scbond_other 4.229 r_mcbond_it 3.711 r_mcbond_other 3.711 r_angle_refined_deg 1.672 r_angle_other_deg 1.318 r_nbd_refined 0.226 r_symmetry_nbd_refined 0.223 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.184 r_nbd_other 0.172 r_metal_ion_refined 0.167 r_xyhbond_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.156 r_chiral_restr 0.132 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28488 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 2742
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling MOLREP phasing