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Catalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides complexed with deoxycholic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GSM PDB entry 2GSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 277 24% PEG-400, 5mM deoxycholic acid , pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.69 66.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.243 α = 90 b = 132.052 β = 90 c = 167.966 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 2007-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9785 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 2.15 50 96.8 0.069 21.9 6.6 150058 145257
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 2.33 77.6 0.513 2.1 3.8 11510
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 THROUGHOUT PDB entry 2GSM 2.15 40 148964 144361 3612 96.91 0.184 0.184 0.184 0.1844 0.212 0.2146 RANDOM 38.516
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 -0.82 2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.681 r_dihedral_angle_4_deg 16.208 r_dihedral_angle_3_deg 13.853 r_dihedral_angle_1_deg 5.681 r_scangle_it 1.965 r_scbond_it 1.376 r_angle_refined_deg 1.215 r_mcangle_it 0.983 r_mcbond_it 0.594 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.681 r_dihedral_angle_4_deg 16.208 r_dihedral_angle_3_deg 13.853 r_dihedral_angle_1_deg 5.681 r_scangle_it 1.965 r_scbond_it 1.376 r_angle_refined_deg 1.215 r_mcangle_it 0.983 r_mcbond_it 0.594 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.127 r_metal_ion_refined 0.108 r_chiral_restr 0.088 r_symmetry_hbond_refined 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12565 Nucleic Acid Atoms Solvent Atoms 636 Heterogen Atoms 780
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing