3SFE

crystal structure of porcine mitochondrial respiratory complex II bound with oxaloacetate and thiabendazole


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.22900.5% n-nonyl-D-maltoside, 1.7mM n-decyl-D-maltoside, 25mM HEPES, 5% PEG 4000, 3% 1,6-hexanediol, 100mM NaCl, 10mM CaCl2, 200mM sucrose, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.5165.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.71α = 90
b = 83.42β = 90
c = 294.01γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.000Photon FactoryBL-17A

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
12.85094.60.1124.54396041586-163.2
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)
12.82.8781.20.4271.73.52859

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1ZOY2.81504158632353171778.060.2740.216840.214050.26985RANDOM56.462
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]
1.07-1.680.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.834
r_dihedral_angle_3_deg18.752
r_dihedral_angle_4_deg14.696
r_dihedral_angle_1_deg5.374
r_angle_refined_deg1.243
r_scangle_it1.019
r_mcangle_it0.608
r_scbond_it0.58
r_mcbond_it0.327
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.834
r_dihedral_angle_3_deg18.752
r_dihedral_angle_4_deg14.696
r_dihedral_angle_1_deg5.374
r_angle_refined_deg1.243
r_scangle_it1.019
r_mcangle_it0.608
r_scbond_it0.58
r_mcbond_it0.327
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8489
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms138

Software

Software
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling