3SFD

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


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
3.4864.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.31α = 90
b = 83.36β = 90
c = 293.1γ = 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
12.65093.90.136208.25369450419-167.7
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)
12.62.6967.80.4761.75.55246

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1ZOY2.615038294205575.340.30.244040.241810.28554RANDOM60.02
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]
-0.29-0.530.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.518
r_dihedral_angle_3_deg18.555
r_dihedral_angle_4_deg16.793
r_dihedral_angle_1_deg5.374
r_angle_refined_deg1.237
r_scangle_it1.1
r_mcangle_it0.672
r_scbond_it0.644
r_mcbond_it0.361
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.518
r_dihedral_angle_3_deg18.555
r_dihedral_angle_4_deg16.793
r_dihedral_angle_1_deg5.374
r_angle_refined_deg1.237
r_scangle_it1.1
r_mcangle_it0.672
r_scbond_it0.644
r_mcbond_it0.361
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8480
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms136

Software

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