3AE5

Crystal structure of porcine heart mitochondrial complex II bound with 2-Methyl-N-(3-isopropoxy-phenyl)-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 DROP829825mM HEPES-NAOH, 8% PEG 4000, 200mM Sucrose, 100mM NaCl, 10mM CaCl2, 0.5mM EDTA, 3% 1,6-haxanediol, 0.5% n-decyl-beta-D-maltoside, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5565.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.098α = 90
b = 83.808β = 90
c = 294.023γ = 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
13.450770.0918.021519023
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)
3.43.5279.70.4981.354.81947

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 1ZOY3.4148.141889993276.310.2310.2280.278RANDOM105.544
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]
-0.130.6-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.581
r_dihedral_angle_3_deg16.525
r_dihedral_angle_4_deg13.911
r_dihedral_angle_1_deg4.417
r_angle_refined_deg0.906
r_scangle_it0.282
r_mcangle_it0.196
r_scbond_it0.158
r_mcbond_it0.106
r_chiral_restr0.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.581
r_dihedral_angle_3_deg16.525
r_dihedral_angle_4_deg13.911
r_dihedral_angle_1_deg4.417
r_angle_refined_deg0.906
r_scangle_it0.282
r_mcangle_it0.196
r_scbond_it0.158
r_mcbond_it0.106
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8480
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms186

Software

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