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Crystal Structure of IDH2 (R140Q) in complex with covalent inhibitor LY3410738
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Internal Structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 100mM Tris pH 7.5, 33% PEG 3350, 200mM Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.06 40.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.721 α = 90 b = 116.643 β = 90 c = 129.207 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2020-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.2 29.6 99.8 0.11 6.3 6.5 44206
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 2.2 2.22 1.17
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 29.57 44207 2175 99.8 0.2249 0.2237 0.2148 0.2472 0.2378 RANDOM 54.05
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] 5.0254 -6.3882 1.3628
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.13 t_omega_torsion 2.92 t_angle_deg 0.89 t_bond_d 0.007 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6305 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 122
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling PHASER phasing