2FYU

Crystal structure of bovine heart mitochondrial bc1 with jg144 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L0N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.2277.250 mM MOPS 7.2pH, 20 mM Ammonium acetate, 20% glycerol.Incubation with 2-5 mol excess of JG144. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57, VAPOR DIFFUSION, SITTING DROP, temperature 277.2K
Crystal Properties
Matthews coefficientSolvent content
3.6466.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.263α = 90
b = 154.263β = 90
c = 590.191γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTORMARRESEARCH2004-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0090NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.265086.10.05617.24157290-0.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.3442.40.3821.813582

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1l0n2.2640157290157290323096.890.249160.249160.248430.28328RANDOM25.239
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]
2.362.36-4.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.115
r_scangle_it7.314
r_scbond_it5.686
r_mcangle_it2.514
r_angle_refined_deg2.063
r_mcbond_it0.592
r_chiral_restr0.2
r_nbd_refined0.117
r_xyhbond_nbd_refined0.096
r_symmetry_vdw_refined0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg11.115
r_scangle_it7.314
r_scbond_it5.686
r_mcangle_it2.514
r_angle_refined_deg2.063
r_mcbond_it0.592
r_chiral_restr0.2
r_nbd_refined0.117
r_xyhbond_nbd_refined0.096
r_symmetry_vdw_refined0.094
r_symmetry_hbond_refined0.068
r_gen_planes_refined0.026
r_bond_refined_d0.021
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16477
Nucleic Acid Atoms
Solvent Atoms267
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling