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Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 277 23%-24% PEG-400, crystals reduced with dithionite and soaked with cyanide, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.9 68.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.344 α = 90 b = 131.877 β = 90 c = 176.16 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 MARMOSAIC 300 mm CCD 2008-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.2 50 95.1 0.072 6.7 145489
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.257 73.5 0.52 3.7
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 2GSM 2.2 50 137425 3933 96.2 0.195 0.1943 0.1933 0.21906 0.2158 RANDOM 44.024
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] -1.73 -0.18 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.904 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_3_deg 13.646 r_dihedral_angle_1_deg 5.533 r_scangle_it 2.161 r_scbond_it 1.342 r_angle_refined_deg 1.155 r_mcangle_it 0.964 r_mcbond_it 0.508 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.904 r_dihedral_angle_4_deg 17.006 r_dihedral_angle_3_deg 13.646 r_dihedral_angle_1_deg 5.533 r_scangle_it 2.161 r_scbond_it 1.342 r_angle_refined_deg 1.155 r_mcangle_it 0.964 r_mcbond_it 0.508 r_nbtor_refined 0.309 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.199 r_metal_ion_refined 0.123 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.082 r_symmetry_hbond_refined 0.062 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12434 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 685
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MD2 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing