☰ Navigation Tabs
Crystal structure of cyanate bound bovine cytochrome c oxidase
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 277 PEG 4000, Potassium Phosphate, Decylmaltoside
Crystal Properties Matthews coefficient Solvent content 4.15 70.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.292 α = 90 b = 182.82 β = 90 c = 208.752 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 2021-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
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 2.1 29.997 100 0.998 10.7 6.8 393869
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 2.1 2.154 99.9 0.51 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 29.997 393869 20057 99.908 0.196 0.1939 0.2011 0.2279 0.2329 48.239
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] -2.808 0.005 2.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 15.696 r_lrange_other 10.157 r_lrange_it 10.155 r_scangle_it 7.245 r_scangle_other 7.245 r_dihedral_angle_1_deg 6.595 r_mcangle_it 5.453 r_mcangle_other 5.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.733 r_dihedral_angle_4_deg 17.771 r_dihedral_angle_3_deg 15.696 r_lrange_other 10.157 r_lrange_it 10.155 r_scangle_it 7.245 r_scangle_other 7.245 r_dihedral_angle_1_deg 6.595 r_mcangle_it 5.453 r_mcangle_other 5.453 r_scbond_it 5.1 r_scbond_other 5.1 r_mcbond_it 3.982 r_mcbond_other 3.981 r_dihedral_angle_other_3_deg 3.866 r_angle_refined_deg 1.733 r_angle_other_deg 1.342 r_symmetry_xyhbond_nbd_refined 0.262 r_nbd_refined 0.221 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.182 r_nbd_other 0.172 r_xyhbond_nbd_refined 0.17 r_symmetry_nbd_refined 0.155 r_symmetry_xyhbond_nbd_other 0.111 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28468 Nucleic Acid Atoms Solvent Atoms 1108 Heterogen Atoms 2757
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing