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Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor WDH-1U-4
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 4.85 74.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.56 α = 90 b = 209.56 β = 90 c = 343.348 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 9M mirrors 2017-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9800 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 3.5 90.74 97.4 0.197 0.219 0.091 0.968 7 5.4 55066
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.6 98.7 0.874 0.966 0.396 0.543 5.5
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 5OKD 3.5 90.74 52188 2800 97.02 0.2186 0.2171 0.2207 0.2457 0.2489 RANDOM 134.235
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] -0.76 -0.38 -0.76 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.649 r_dihedral_angle_3_deg 16.293 r_dihedral_angle_4_deg 14.914 r_dihedral_angle_1_deg 5.625 r_angle_refined_deg 1.437 r_chiral_restr 0.091 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15617 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 588
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction