4YTP

CRYSTAL STRUCTURE OF PORCINE HEART MITOCHONDRIAL COMPLEX II BOUND WITH N-[(4-tert-butylphenyl)methyl]-2-(trifluoromethyl)benzamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.42935MM HEPES-NAOH, 7% PEG 4000, 200MM SUCROSE, 100MM NACL, 10MM CACL2, 0.5MM EDTA, 3% 1,6-HAXANEDIOL,0.5% N-DECYL-BETA-D-MALTOSIDE
Crystal Properties
Matthews coefficientSolvent content
3.1661.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.429α = 90
b = 84.008β = 90
c = 294.817γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702013-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.98000Photon 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
13.15093.30.09511.43.931105
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)
13.13.1594.90.5161.74.6

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 REPLACEMENTTHROUGHOUT1ZOY3.12025461135280.740.209540.206380.26903RANDOM70.325
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]
2.55-1.16-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.755
r_dihedral_angle_3_deg18.588
r_dihedral_angle_4_deg18.389
r_dihedral_angle_1_deg6.33
r_angle_refined_deg1.227
r_angle_other_deg0.838
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.755
r_dihedral_angle_3_deg18.588
r_dihedral_angle_4_deg18.389
r_dihedral_angle_1_deg6.33
r_angle_refined_deg1.227
r_angle_other_deg0.838
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_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 Atoms22
Heterogen Atoms139

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing