5LGE

Crystal Structure of human IDH1 mutant (R132H) in complex with NADP+ and an Inhibitor related to BAY 1436032


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7293PROTEIN BUFFER: 15 MG/ML. PROTEIN IN 25 MM HEPES, 300 MM NACL, 5 MM BETA-ME, COMPLETE PROTEASE INHIBITOR MIXTURE, PH 7.7 RESERVOIR: 100 MM BIS-TRIS, PH 7.0, 200 MM CA-ACETATE, 20.0 %(W/V) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7655.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.9α = 90
b = 110.32β = 91.19
c = 198.54γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93PIXELDECTRIS PILATUS 6M-F2013-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
12.73098.70.128.64.8566252
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)
12.72.85990.72.34.8

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 REPLACEMENTTHROUGHOUT4KZO2.729.9453784283998.530.197220.195460.22977RANDOM73.2
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]
-0.030.48-0.430.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.606
r_dihedral_angle_4_deg20.556
r_dihedral_angle_3_deg17.938
r_dihedral_angle_1_deg6.319
r_long_range_B_refined5.967
r_long_range_B_other5.89
r_mcangle_it2.718
r_mcangle_other2.718
r_scangle_other2.571
r_mcbond_it1.532
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.606
r_dihedral_angle_4_deg20.556
r_dihedral_angle_3_deg17.938
r_dihedral_angle_1_deg6.319
r_long_range_B_refined5.967
r_long_range_B_other5.89
r_mcangle_it2.718
r_mcangle_other2.718
r_scangle_other2.571
r_mcbond_it1.532
r_mcbond_other1.532
r_angle_refined_deg1.484
r_scbond_it1.454
r_scbond_other1.454
r_angle_other_deg1.317
r_chiral_restr0.079
r_bond_refined_d0.009
r_bond_other_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12995
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms270

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing