3AE9

Crystal structure of porcine heart mitochondrial complex II bound with N-(3-Pentafluorophenyloxy-phenyl)-2-trifluoromethyl-benzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZOYPDB ENTRY 1ZOY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.229325mM HEPES-NAOH, 6% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6766.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.609α = 90
b = 84.249β = 90
c = 295.646γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.35098.20.0812.783427349
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)
13.33.4299.40.4661.984.12716

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1ZOY3.3137.7627275136797.830.2590.2570.307RANDOM124.638
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]
1.69-0.48-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.628
r_dihedral_angle_3_deg15.482
r_dihedral_angle_4_deg10.189
r_dihedral_angle_1_deg4.045
r_angle_refined_deg0.867
r_mcangle_it0.216
r_scangle_it0.198
r_mcbond_it0.12
r_scbond_it0.111
r_chiral_restr0.055
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.628
r_dihedral_angle_3_deg15.482
r_dihedral_angle_4_deg10.189
r_dihedral_angle_1_deg4.045
r_angle_refined_deg0.867
r_mcangle_it0.216
r_scangle_it0.198
r_mcbond_it0.12
r_scbond_it0.111
r_chiral_restr0.055
r_bond_refined_d0.005
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8480
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms197

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing