6XVF

Crystal structure of bovine cytochrome bc1 in complex with tetrahydro-quinolone inhibitor JAG021


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OKD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8277Protein 40mg/mL with 1.6% HECAMEG; Reservoir solution: 50mM KPi pH 6.8, 100mM NaCl, 3mM NaN3, 10-13% PEG4000
Crystal Properties
Matthews coefficientSolvent content
4.8674.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.869α = 90
b = 209.869β = 90
c = 342.418γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9Mmirrors2017-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.9801SOLEILPROXIMA 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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.4590.8891.40.2250.2350.0680.9998.611.45352694.4
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)RedundancyNumber Unique Reflections (All)
13.453.5692.81.1110.3340.2952.411.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5OKD3.590.8848681258390.410.21810.21740.2324RANDOM165.129
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]
-0.09-0.05-0.090.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.261
r_dihedral_angle_3_deg16.312
r_dihedral_angle_4_deg14.392
r_dihedral_angle_1_deg5.72
r_angle_refined_deg1.426
r_chiral_restr0.091
r_bond_refined_d0.008
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15505
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms597

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing