5GRL

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES-Na, pH 7.5, 12% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.4464.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.238α = 90
b = 111.238β = 90
c = 145.478γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97915SSRFBL19U1

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
12.795098.114.52.825878
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.9

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 REPLACEMENTTHROUGHOUT5GRI2.795024151128496.470.22860.22620.2736RANDOM39.353
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]
0.080.040.08-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.088
r_dihedral_angle_4_deg17.844
r_dihedral_angle_3_deg15.663
r_dihedral_angle_1_deg5.703
r_mcangle_it3.654
r_mcbond_it2.267
r_mcbond_other2.262
r_angle_refined_deg1.11
r_angle_other_deg0.88
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.088
r_dihedral_angle_4_deg17.844
r_dihedral_angle_3_deg15.663
r_dihedral_angle_1_deg5.703
r_mcangle_it3.654
r_mcbond_it2.267
r_mcbond_other2.262
r_angle_refined_deg1.11
r_angle_other_deg0.88
r_chiral_restr0.057
r_bond_refined_d0.006
r_bond_other_d0.006
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5035
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing