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Crystal Structure of IDH2 (R172K) 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 295 100mM Tris pH 8.5, 25% PEG 3350, 200mM Sodium Chloride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.121 α = 90 b = 112.501 β = 90 c = 124.498 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 6M 2020-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9840 ESRF ID30B
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 19.7 96.3 0.17 3.1 3.5 53256
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 2.05 0.859
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 19.71 52687 2610 95.8 0.2155 0.2142 0.2053 0.241 0.2363 RANDOM 36.91
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] 3.1423 -3.3496 0.2073
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.79 t_omega_torsion 3.24 t_angle_deg 0.96 t_bond_d 0.008 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 6467 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 122
Software Software Software Name Purpose BUSTER refinement XDS data reduction Aimless data scaling