8HB9

Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6B0Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP31524% PEG 3350, 8% Tacsimate pH 6.0
Crystal Properties
Matthews coefficientSolvent content
3.0559.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.759α = 90
b = 76.426β = 98.27
c = 171.971γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2022-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5406

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
12.813.078990.118.84.153443
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)
12.82.890.606

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6b0z2.813.07853423262498.8550.2180.21650.243341.89
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]
-2.0250.3323.625-1.628
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.821
r_dihedral_angle_4_deg17.367
r_dihedral_angle_3_deg14.624
r_dihedral_angle_1_deg5.679
r_lrange_it3.928
r_lrange_other3.909
r_dihedral_angle_other_2_deg2.94
r_mcangle_it2.088
r_mcangle_other2.088
r_chiral_restr_other1.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.821
r_dihedral_angle_4_deg17.367
r_dihedral_angle_3_deg14.624
r_dihedral_angle_1_deg5.679
r_lrange_it3.928
r_lrange_other3.909
r_dihedral_angle_other_2_deg2.94
r_mcangle_it2.088
r_mcangle_other2.088
r_chiral_restr_other1.778
r_scangle_it1.685
r_scangle_other1.685
r_angle_refined_deg1.227
r_angle_other_deg1.171
r_mcbond_it1.168
r_mcbond_other1.166
r_scbond_it0.913
r_scbond_other0.913
r_nbd_other0.198
r_nbd_refined0.167
r_symmetry_nbd_other0.15
r_nbtor_refined0.15
r_xyhbond_nbd_refined0.128
r_symmetry_nbd_refined0.126
r_symmetry_xyhbond_nbd_refined0.104
r_ncsr_local_group_30.082
r_symmetry_nbtor_other0.08
r_ncsr_local_group_50.079
r_ncsr_local_group_10.075
r_ncsr_local_group_60.075
r_ncsr_local_group_20.071
r_ncsr_local_group_40.07
r_symmetry_xyhbond_nbd_other0.051
r_chiral_restr0.037
r_bond_refined_d0.004
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12782
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms269

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing