5GRE

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.2 M sodium citrate, pH 8.0, 20% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.0860

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 104.91α = 90
b = 104.91β = 90
c = 146.25γ = 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 BL19U11.0000SSRFBL19U1

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
12.655099.922.49.127500
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.74

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 REPLACEMENTTHROUGHOUT5GRI2.6545.4326073138299.730.19710.19470.2414RANDOM49.333
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]
3.693.69-7.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.226
r_dihedral_angle_4_deg18.568
r_dihedral_angle_3_deg17.339
r_mcangle_it6.877
r_dihedral_angle_1_deg5.694
r_mcbond_it4.709
r_mcbond_other4.679
r_angle_refined_deg1.347
r_angle_other_deg1.01
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.226
r_dihedral_angle_4_deg18.568
r_dihedral_angle_3_deg17.339
r_mcangle_it6.877
r_dihedral_angle_1_deg5.694
r_mcbond_it4.709
r_mcbond_other4.679
r_angle_refined_deg1.347
r_angle_other_deg1.01
r_chiral_restr0.081
r_bond_refined_d0.009
r_bond_other_d0.007
r_gen_planes_refined0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5042
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing