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Crystal structure of bovine cytochrome bc1 in complex with tetrahydro-quinolone inhibitor JAG021
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 277 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 4.86 74.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.869 α = 90 b = 209.869 β = 90 c = 342.418 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 EIGER2 X 9M mirrors 2017-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.45 90.88 91.4 0.225 0.235 0.068 0.999 8.6 11.4 53526 94.4
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 3.45 3.56 92.8 1.111 0.334 0.295 2.4 11.6
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 5OKD 3.5 90.88 48681 2583 90.41 0.2181 0.2174 0.2222 0.2324 0.2378 RANDOM 165.129
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] -0.09 -0.05 -0.09 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.261 r_dihedral_angle_3_deg 16.312 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_1_deg 5.72 r_angle_refined_deg 1.426 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15505 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 597
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing