7R3V

Crystal structure of bovine Cytochrome bc1 in complex with inhibitor CK-2-67.


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, 9-12% PEG4000
Crystal Properties
Matthews coefficientSolvent content
4.7273.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.589α = 90
b = 209.589β = 90
c = 342.429γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9786SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.249.8697.20.2250.0640.9931.79.470108
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)
13.23.2797.21.5971.7180.4980.4151.74.9

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 REPLACEMENTTHROUGHOUT5OKD3.249.8666560344395.080.207610.205090.25556RANDOM86.4
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]
-1.26-0.63-1.264.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.886
r_long_range_B_refined20.812
r_dihedral_angle_3_deg19.531
r_dihedral_angle_4_deg18.667
r_mcangle_it13.943
r_scbond_it10.09
r_mcbond_it9.226
r_dihedral_angle_1_deg7.146
r_angle_refined_deg1.732
r_chiral_restr0.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.886
r_long_range_B_refined20.812
r_dihedral_angle_3_deg19.531
r_dihedral_angle_4_deg18.667
r_mcangle_it13.943
r_scbond_it10.09
r_mcbond_it9.226
r_dihedral_angle_1_deg7.146
r_angle_refined_deg1.732
r_chiral_restr0.114
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15778
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms559

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing