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Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 40 mM sodium phosphate pH 6.8, 0.2% decylmaltoside, 1% polyethylene glycol 4000, 2% ethylene glycol
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.998 α = 90 b = 204.193 β = 90 c = 177.759 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 60 CCD RAYONIX MX225HE 2012-06-29 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) Rpim 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 1.3 200 100 0.03 0.55 39.7 13.4 1596005
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.31 0.94
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 5B1A 1.3 40 1510822 79183 99.58 0.1496 0.1485 0.161 0.1704 0.1801 RANDOM 30.499
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] 0.46 -1.58 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.911 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 13.983 r_dihedral_angle_1_deg 6.172 r_rigid_bond_restr 5.786 r_angle_refined_deg 2.27 r_angle_other_deg 1.526 r_chiral_restr 0.466 r_bond_refined_d 0.021 r_gen_planes_refined 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.911 r_dihedral_angle_4_deg 15.271 r_dihedral_angle_3_deg 13.983 r_dihedral_angle_1_deg 6.172 r_rigid_bond_restr 5.786 r_angle_refined_deg 2.27 r_angle_other_deg 1.526 r_chiral_restr 0.466 r_bond_refined_d 0.021 r_gen_planes_refined 0.015 r_gen_planes_other 0.006 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27834 Nucleic Acid Atoms Solvent Atoms 2080 Heterogen Atoms 2608
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling REFMAC phasing