3AEE

Crystal structure of porcine heart mitochondrial complex II bound with Atpenin A5


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, 5% 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
3.5365.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.751α = 90
b = 83.841β = 90
c = 293.735γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-12-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.80000Photon FactoryAR-NW12A

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
13.25095.70.07915.6573.827959
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)
3.23.3197.40.4882.43.72770

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 1ZOY3.2248.9627888143695.280.2350.2320.282RANDOM106.185
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]
0.710.09-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.032
r_dihedral_angle_3_deg19.184
r_dihedral_angle_4_deg17.217
r_dihedral_angle_1_deg5.477
r_angle_refined_deg1.11
r_scangle_it0.839
r_scbond_it0.481
r_mcangle_it0.463
r_mcbond_it0.248
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.032
r_dihedral_angle_3_deg19.184
r_dihedral_angle_4_deg17.217
r_dihedral_angle_1_deg5.477
r_angle_refined_deg1.11
r_scangle_it0.839
r_scbond_it0.481
r_mcangle_it0.463
r_mcbond_it0.248
r_chiral_restr0.078
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8480
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms138

Software

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