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Bovine Heart Cytochrome c Oxidase in the Xenon-bound Fully Oxidized State under Anaerobic Condition
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 69.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.9 α = 90 b = 204 β = 90 c = 178 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 2024-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.0 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 1.8 200 100 0.051 1 38.8 21.2 1185920 28.9
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 1.8 1.85 100 0.86 0.964 4.48 20
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 1.8 40 575456 30179 99.98 0.12188 0.12014 0.1376 0.15484 0.1652 RANDOM 40.514
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] -0.01 2.7 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.624 r_dihedral_angle_4_deg 15.248 r_dihedral_angle_3_deg 13.762 r_scangle_other 6.921 r_scbond_it 6.183 r_scbond_other 6.183 r_long_range_B_refined 6.18 r_long_range_B_other 6.124 r_dihedral_angle_1_deg 6.042 r_mcangle_it 4.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.624 r_dihedral_angle_4_deg 15.248 r_dihedral_angle_3_deg 13.762 r_scangle_other 6.921 r_scbond_it 6.183 r_scbond_other 6.183 r_long_range_B_refined 6.18 r_long_range_B_other 6.124 r_dihedral_angle_1_deg 6.042 r_mcangle_it 4.338 r_mcangle_other 4.338 r_rigid_bond_restr 3.971 r_mcbond_it 3.872 r_mcbond_other 3.871 r_angle_refined_deg 1.903 r_angle_other_deg 1.475 r_chiral_restr 0.453 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.005 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 2005 Heterogen Atoms 2604
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing