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Bovine Heart Cytochrome c Oxidase in the Carbon Dioxide-bound Fully Reduced State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8R8S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 40 mM sodium phosphate buffer, pH 6.8 0.2% (w/v) decyl-maltoside 1% (w/v) polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 4.21 70.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.7 α = 90 b = 205.1 β = 90 c = 177.6 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 90 PIXEL DECTRIS EIGER X 16M 2024-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.85 200 100 0.117 0.999 15.7 17.7 1100575 31.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 100 2.43 0.741 1.31 16.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8R8S 1.85 40 534393 27946 99.98 0.13495 0.1331 0.1474 0.17028 0.1783 RANDOM 42.774
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] -0.56 4.69 -4.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.27 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 14.058 r_scangle_other 6.959 r_long_range_B_refined 6.388 r_long_range_B_other 6.334 r_dihedral_angle_1_deg 6.195 r_scbond_it 6.111 r_scbond_other 6.111 r_mcangle_other 4.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.27 r_dihedral_angle_4_deg 15.268 r_dihedral_angle_3_deg 14.058 r_scangle_other 6.959 r_long_range_B_refined 6.388 r_long_range_B_other 6.334 r_dihedral_angle_1_deg 6.195 r_scbond_it 6.111 r_scbond_other 6.111 r_mcangle_other 4.58 r_mcangle_it 4.579 r_mcbond_it 4.04 r_mcbond_other 4.039 r_rigid_bond_restr 3.681 r_angle_refined_deg 1.872 r_angle_other_deg 1.433 r_chiral_restr 0.448 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27834 Nucleic Acid Atoms Solvent Atoms 2001 Heterogen Atoms 2592
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing