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Bovine Heart Cytochrome c Oxidase in the Calcium-bound Fully Oxidized State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7COH
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 4.08 69.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.8 α = 90 b = 205.7 β = 90 c = 177.9 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 2018-06-28 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 1.7 200 99.8 0.085 0.997 14.1 8.7 691219 32.1
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 1.7 1.74 97.9 1.38 0.78 1.6 8.4
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 7COH 1.7 40 691219 36109 99.97 0.12419 0.12265 0.1394 0.15306 0.1647 RANDOM 42.188
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] -1.79 2.65 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 15.598 r_dihedral_angle_3_deg 13.887 r_scangle_other 7.38 r_long_range_B_refined 6.696 r_long_range_B_other 6.625 r_scbond_it 6.569 r_scbond_other 6.569 r_dihedral_angle_1_deg 6.073 r_mcangle_it 4.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 15.598 r_dihedral_angle_3_deg 13.887 r_scangle_other 7.38 r_long_range_B_refined 6.696 r_long_range_B_other 6.625 r_scbond_it 6.569 r_scbond_other 6.569 r_dihedral_angle_1_deg 6.073 r_mcangle_it 4.62 r_mcangle_other 4.62 r_mcbond_it 4.095 r_mcbond_other 4.092 r_rigid_bond_restr 3.864 r_angle_refined_deg 1.841 r_angle_other_deg 1.459 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 2590
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling MOLREP phasing