☰ Navigation Tabs
Structure of reduced bovine cytochrome c oxidase at 1.93 Angstrom resolution obtained by synchrotron X-rays
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.8 277 PEG 4000, Postassium phosphate, Decylmaltoside
Crystal Properties Matthews coefficient Solvent content 4.13 70.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.182 α = 90 b = 182.282 β = 90 c = 208.683 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 PIXEL DECTRIS PILATUS 6M 2019-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.93 40.003 99.2 0.999 12.6 6.8 500705
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.03 0.416 1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2DYR 1.93 40.003 500554 24681 99.129 0.185 0.1836 0.1936 0.2125 0.2197 46.817
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] -2.323 -0.727 3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.506 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_other_3_deg 16.375 r_dihedral_angle_3_deg 16.33 r_lrange_other 9.075 r_lrange_it 9.072 r_scangle_it 7.166 r_scangle_other 7.165 r_dihedral_angle_1_deg 6.422 r_mcangle_it 4.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.506 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_other_3_deg 16.375 r_dihedral_angle_3_deg 16.33 r_lrange_other 9.075 r_lrange_it 9.072 r_scangle_it 7.166 r_scangle_other 7.165 r_dihedral_angle_1_deg 6.422 r_mcangle_it 4.968 r_mcangle_other 4.968 r_scbond_it 4.965 r_scbond_other 4.965 r_mcbond_it 3.641 r_mcbond_other 3.641 r_chiral_restr_other 2.042 r_angle_refined_deg 1.809 r_angle_other_deg 1.424 r_nbd_other 0.225 r_nbd_refined 0.214 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_other 0.177 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.143 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28584 Nucleic Acid Atoms Solvent Atoms 1381 Heterogen Atoms 2730
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing