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Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state
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, crystal reduced by dithionite, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.9 68.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.613 α = 90 b = 131.472 β = 90 c = 176.192 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 2007-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.12 50 98.5 0.066 4.6 162159
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) 2.15 2.206 92.7 0.606 4 10331
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.15 50 151414 151414 4375 99.09 0.196 0.196 0.196 0.1968 0.221 0.2207 RANDOM 45.8
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] -2.03 -0.22 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.07 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 5.667 r_scangle_it 2.042 r_scbond_it 1.432 r_angle_refined_deg 1.227 r_mcangle_it 1.025 r_mcbond_it 0.625 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.07 r_dihedral_angle_4_deg 18.729 r_dihedral_angle_3_deg 13.707 r_dihedral_angle_1_deg 5.667 r_scangle_it 2.042 r_scbond_it 1.432 r_angle_refined_deg 1.227 r_mcangle_it 1.025 r_mcbond_it 0.625 r_nbtor_refined 0.31 r_symmetry_hbond_refined 0.207 r_symmetry_vdw_refined 0.203 r_nbd_refined 0.196 r_metal_ion_refined 0.127 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12452 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 679
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing