5YVT

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and NADH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GRH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES-Na, pH 7.5, 50 mM MgCl2, 30% (v/v) PEGMME 550
Crystal Properties
Matthews coefficientSolvent content
3.7867.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.027α = 90
b = 118.027β = 90
c = 142.109γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9785SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.45010022.69.945428
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.491002.88.9

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 REPLACEMENTTHROUGHOUT5GRH2.45043063232399.930.21260.211360.23637RANDOM64.145
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]
1.40.71.4-4.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.998
r_dihedral_angle_4_deg23.149
r_dihedral_angle_3_deg15.806
r_long_range_B_refined6.281
r_dihedral_angle_1_deg5.502
r_mcangle_it3.165
r_scbond_it2.246
r_mcbond_it1.856
r_angle_refined_deg1.296
r_chiral_restr0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.998
r_dihedral_angle_4_deg23.149
r_dihedral_angle_3_deg15.806
r_long_range_B_refined6.281
r_dihedral_angle_1_deg5.502
r_mcangle_it3.165
r_scbond_it2.246
r_mcbond_it1.856
r_angle_refined_deg1.296
r_chiral_restr0.08
r_bond_refined_d0.008
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
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 Atoms5048
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms89

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PHASERphasing