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Bovine heart cytochrome c oxidase in the reduced state with pH 7.3 at 1.99 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.3 277 3% PEG 1500, 0.20% decal maltoside, 0.35% fluorinated octyl-maltoside, 25mM Tris-HCL(pH 7.3), 20mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 4.15 70.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.044 α = 90 b = 205.691 β = 90 c = 177.797 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 100 CCD RAYONIX MX-225 2014-11-15 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) Rrim I (All) Rpim I (All) 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 1.98 200 99.9 0.112 0.114 0.025 11.7 14.2 457705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2 99.6 0.996 0.423 0.751 6.2
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 1V55 1.99 40 434234 23137 99.65 0.1832 0.1822 0.1836 0.2025 0.2062 RANDOM 49.372
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] -0.18 4.08 -3.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.567 r_dihedral_angle_4_deg 15.118 r_dihedral_angle_3_deg 14.029 r_sphericity_bonded 6.16 r_rigid_bond_restr 6.132 r_dihedral_angle_1_deg 5.29 r_angle_refined_deg 1.259 r_chiral_restr 0.085 r_gen_planes_refined 0.021 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28450 Nucleic Acid Atoms Solvent Atoms 1942 Heterogen Atoms 2424
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing