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Bovine heart cytochrome c oxidase in the fully oxidized state with pH 7.3 at 1.77 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V54
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.3 277 3% polythylene glycol (PEG), 0.35% decal maltose, 0.70% fluorinated octyl-maltoside, 33mM sodium acetate, 25mM Tris-HCL (pH 7.3)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.307 α = 90 b = 205.904 β = 90 c = 177.526 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 50 CCD RAYONIX MX-225 2014-07-09 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) R Merge I (Observed) 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 1.77 200 99.9 0.086 13 8.9 643861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.79 100 8.2 16039
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 1V54 1.77 134.453 611017 32361 99.59 0.1652 0.1639 0.1664 0.1904 0.1916 RANDOM 45.057
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] -0.29 6.37 -6.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.805 r_sphericity_free 25.121 r_sphericity_bonded 23.645 r_dihedral_angle_3_deg 13.76 r_dihedral_angle_4_deg 13.607 r_dihedral_angle_1_deg 5.164 r_rigid_bond_restr 2.409 r_angle_refined_deg 1.203 r_chiral_restr 0.082 r_gen_planes_refined 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.805 r_sphericity_free 25.121 r_sphericity_bonded 23.645 r_dihedral_angle_3_deg 13.76 r_dihedral_angle_4_deg 13.607 r_dihedral_angle_1_deg 5.164 r_rigid_bond_restr 2.409 r_angle_refined_deg 1.203 r_chiral_restr 0.082 r_gen_planes_refined 0.02 r_bond_refined_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28442 Nucleic Acid Atoms Solvent Atoms 2883 Heterogen Atoms 2542
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing