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Crystal structure of bovine Cytochrome bc1 in complex with inhibitor SCR0911.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Protein 40mg/mL with 1.6% HECAMEG; reservoir solution 50mM KPi pH 6.8, 100mM NaCl, 3mM NaN3, 10-13% PEG4000
Crystal Properties Matthews coefficient Solvent content 4.41 72.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.871 α = 90 b = 209.871 β = 90 c = 342.097 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 PILATUS 6M mirrors 2017-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.00 Diamond I03
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 3.1 89 99.5 0.104 0.043 0.977 12.3 7.4 80268 71.303
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.16 99.9 1.126 0.655 0.572 1.8 7.5
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 (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 4d6t 3.1 31.76 76127 4037 99.03 0.20641 0.20462 0.2073 0.23993 0.239 RANDOM 101.1
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] 0.03 0.02 0.03 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.408 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_4_deg 13.122 r_dihedral_angle_1_deg 5.849 r_long_range_B_other 4.604 r_long_range_B_refined 4.603 r_scangle_other 2.08 r_mcangle_it 1.951 r_mcangle_other 1.951 r_angle_refined_deg 1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.408 r_dihedral_angle_3_deg 15.124 r_dihedral_angle_4_deg 13.122 r_dihedral_angle_1_deg 5.849 r_long_range_B_other 4.604 r_long_range_B_refined 4.603 r_scangle_other 2.08 r_mcangle_it 1.951 r_mcangle_other 1.951 r_angle_refined_deg 1.26 r_scbond_it 1.196 r_scbond_other 1.196 r_mcbond_it 1.113 r_mcbond_other 1.113 r_angle_other_deg 0.887 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15787 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 601
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling MOLREP phasing