6O2Y | pdb_00006o2y

Crystal structure of IDH1 R132H mutant in complex with compound 24


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG MME 5000, 0.1 M Bicine pH 8.5, and 0.2 M Sodium formate.
Crystal Properties
Matthews coefficientSolvent content
2.5852.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 165.679α = 90
b = 63.496β = 99.52
c = 143.598γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0750NSLSX29A

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
12.85098.615.82.836650
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 methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.85034299180398.280.211990.208590.210.27450.27RANDOM
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]
-0.230.94-2.041.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.923
r_dihedral_angle_4_deg23.748
r_dihedral_angle_3_deg21.752
r_dihedral_angle_1_deg7.015
r_long_range_B_refined4.637
r_long_range_B_other4.637
r_angle_other_deg3.79
r_mcangle_it1.851
r_mcangle_other1.851
r_scangle_other1.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.923
r_dihedral_angle_4_deg23.748
r_dihedral_angle_3_deg21.752
r_dihedral_angle_1_deg7.015
r_long_range_B_refined4.637
r_long_range_B_other4.637
r_angle_other_deg3.79
r_mcangle_it1.851
r_mcangle_other1.851
r_scangle_other1.634
r_angle_refined_deg1.565
r_mcbond_it1.045
r_mcbond_other1.045
r_scbond_it0.954
r_scbond_other0.954
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_other_d
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 Atoms9735
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing