6ZFT

Crystal structure of bovine cytochrome bc1 in complex with quinolone inhibitor CK-2-68


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
5.0275.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 212.36α = 90
b = 212.36β = 90
c = 345.914γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-Fmirrors2017-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9282DiamondI04

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
13.391.9570.40.1710.1810.0570.9986.98.948418
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)RedundancyNumber Unique Reflections (All)
13.33.41731.4021.4870.4730.3578.9

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 REPLACEMENTTHROUGHOUT5OKD3.360.9245958244569.480.21550.2140.2442RANDOM99.187
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]
0.930.470.93-3.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.083
r_dihedral_angle_3_deg16.362
r_dihedral_angle_4_deg12.511
r_dihedral_angle_1_deg6.673
r_angle_refined_deg1.463
r_angle_other_deg1.113
r_chiral_restr0.18
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.083
r_dihedral_angle_3_deg16.362
r_dihedral_angle_4_deg12.511
r_dihedral_angle_1_deg6.673
r_angle_refined_deg1.463
r_angle_other_deg1.113
r_chiral_restr0.18
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15641
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms610

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction