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Bovine Heart Cytochrome c Oxidase in the Nitrous Oxide-bound Fully Oxidized State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8H8R
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 4.03 69.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.1 α = 90 b = 204.3 β = 90 c = 177.8 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 2023-10-26 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 1.75 200 100 0.113 0.999 14.1 14.2 1292429 29.3
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 1.75 1.8 100 2.91 0.695 1.19 14.5
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 8H8R 1.75 40 626789 32888 99.98 0.13979 0.13801 0.1526 0.17352 0.1821 RANDOM 39.468
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] -1.64 5.75 -4.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.705 r_dihedral_angle_4_deg 15.35 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_1_deg 6.155 r_scangle_other 5.881 r_long_range_B_refined 5.357 r_long_range_B_other 5.314 r_scbond_it 5.204 r_scbond_other 5.204 r_mcangle_other 4.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.705 r_dihedral_angle_4_deg 15.35 r_dihedral_angle_3_deg 13.986 r_dihedral_angle_1_deg 6.155 r_scangle_other 5.881 r_long_range_B_refined 5.357 r_long_range_B_other 5.314 r_scbond_it 5.204 r_scbond_other 5.204 r_mcangle_other 4.006 r_mcangle_it 4.005 r_rigid_bond_restr 3.773 r_mcbond_it 3.582 r_mcbond_other 3.581 r_angle_refined_deg 1.951 r_angle_other_deg 1.468 r_chiral_restr 0.452 r_bond_refined_d 0.016 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 2007 Heterogen Atoms 2596
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing