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Bovine Heart Cytochrome c Oxidase in the Nitrous Oxide-bound Fully Reduced State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8H8S
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 4.02 69.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.9 α = 90 b = 204 β = 90 c = 177.7 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 2023-11-19 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 0.118 1 22.2 14 1288078 31.1
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 99.9 0.394 0.748 1.25 14
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 8H8S 1.75 40 624771 32773 99.97 0.15478 0.15297 0.1654 0.18902 0.198 RANDOM 39.829
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] -2.76 8.13 -5.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 14.082 r_dihedral_angle_1_deg 6.294 r_scangle_other 5.203 r_long_range_B_refined 4.987 r_long_range_B_other 4.955 r_scbond_it 4.612 r_scbond_other 4.612 r_mcangle_it 3.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_dihedral_angle_4_deg 16.61 r_dihedral_angle_3_deg 14.082 r_dihedral_angle_1_deg 6.294 r_scangle_other 5.203 r_long_range_B_refined 4.987 r_long_range_B_other 4.955 r_scbond_it 4.612 r_scbond_other 4.612 r_mcangle_it 3.856 r_mcangle_other 3.856 r_rigid_bond_restr 3.831 r_mcbond_it 3.407 r_mcbond_other 3.407 r_angle_refined_deg 2.056 r_angle_other_deg 1.471 r_chiral_restr 0.453 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.002 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