5I95

Crystal Structure of Human Mitochondrial Isocitrate Dehydrogenase R140Q Mutant Homodimer bound to NADPH and alpha-Ketoglutaric acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JA8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291200 mM magnesium acetate, 100 mM sodium cacodylate, pH 6.5, 20% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.6152.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.178α = 90
b = 154.875β = 90
c = 93.57γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97916SSRFBL17U

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
11.5429.8399.50.07810.54.872657
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)
11.541.698.30.5344.3

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 REPLACEMENTTHROUGHOUT4JA81.5429.8368300362499.370.14380.14220.1742RANDOM17.449
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.893
r_dihedral_angle_4_deg20.146
r_dihedral_angle_3_deg12.933
r_dihedral_angle_1_deg6.281
r_angle_refined_deg2.431
r_mcangle_it2.277
r_mcbond_it1.597
r_mcbond_other1.592
r_angle_other_deg1.362
r_chiral_restr0.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.893
r_dihedral_angle_4_deg20.146
r_dihedral_angle_3_deg12.933
r_dihedral_angle_1_deg6.281
r_angle_refined_deg2.431
r_mcangle_it2.277
r_mcbond_it1.597
r_mcbond_other1.592
r_angle_other_deg1.362
r_chiral_restr0.147
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3281
Nucleic Acid Atoms
Solvent Atoms591
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction