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Crystal structure of bovine Cytochrome bc1 in complex with inhibitor F8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 277 50 mM KPi pH 6.8, 100 mM NaCl, 3 mM NaN3, 10-20% PEG4000
Crystal Properties Matthews coefficient Solvent content 4.83 74.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.082 α = 90 b = 210.082 β = 90 c = 344.844 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER X 16M 2020-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97856 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.52 49.65 99.6 0.15 0.05 0.99 13.5 10.3 55657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.54 3.62 96.5 0.51 0.54 1.6
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 3.522 30 55657 2830 99.106 0.19 0.1877 0.1878 0.2407 0.2407 124.215
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] -0.316 -0.158 -0.316 1.026
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.372 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_2_deg 16.924 r_scangle_it 15.641 r_dihedral_angle_6_deg 14.327 r_mcangle_it 11.98 r_scbond_it 10.54 r_mcbond_it 7.758 r_dihedral_angle_1_deg 7.5 r_angle_refined_deg 2.081
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 19.372 r_dihedral_angle_3_deg 16.96 r_dihedral_angle_2_deg 16.924 r_scangle_it 15.641 r_dihedral_angle_6_deg 14.327 r_mcangle_it 11.98 r_scbond_it 10.54 r_mcbond_it 7.758 r_dihedral_angle_1_deg 7.5 r_angle_refined_deg 2.081 r_symmetry_xyhbond_nbd_refined 0.383 r_nbtor_refined 0.318 r_nbd_refined 0.237 r_symmetry_nbd_refined 0.235 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.133 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15866 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 813
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing