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Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B0Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 315 24% PEG 3350, 8% Tacsimate pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.759 α = 90 b = 76.426 β = 98.27 c = 171.971 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K 2022-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 13.078 99 0.11 8.8 4.1 53443
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.89 0.606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6b0z 2.8 13.078 53423 2624 98.855 0.218 0.2165 0.2196 0.2433 0.2458 41.89
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] -2.025 0.332 3.625 -1.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 14.624 r_dihedral_angle_1_deg 5.679 r_lrange_it 3.928 r_lrange_other 3.909 r_dihedral_angle_other_2_deg 2.94 r_mcangle_it 2.088 r_mcangle_other 2.088 r_chiral_restr_other 1.778
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.821 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 14.624 r_dihedral_angle_1_deg 5.679 r_lrange_it 3.928 r_lrange_other 3.909 r_dihedral_angle_other_2_deg 2.94 r_mcangle_it 2.088 r_mcangle_other 2.088 r_chiral_restr_other 1.778 r_scangle_it 1.685 r_scangle_other 1.685 r_angle_refined_deg 1.227 r_angle_other_deg 1.171 r_mcbond_it 1.168 r_mcbond_other 1.166 r_scbond_it 0.913 r_scbond_other 0.913 r_nbd_other 0.198 r_nbd_refined 0.167 r_symmetry_nbd_other 0.15 r_nbtor_refined 0.15 r_xyhbond_nbd_refined 0.128 r_symmetry_nbd_refined 0.126 r_symmetry_xyhbond_nbd_refined 0.104 r_ncsr_local_group_3 0.082 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_5 0.079 r_ncsr_local_group_1 0.075 r_ncsr_local_group_6 0.075 r_ncsr_local_group_2 0.071 r_ncsr_local_group_4 0.07 r_symmetry_xyhbond_nbd_other 0.051 r_chiral_restr 0.037 r_bond_refined_d 0.004 r_bond_other_d 0.003 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12782 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 269
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing