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Discovery of an Orally Biovailable KRAS G12D Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M (NH4)3 Citrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.41 48.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.04 α = 90 b = 53.71 β = 90 c = 88.85 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 EIGER2 X 9M 2021-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.36 45.96 87 0.063 0.069 0.027 0.998 14.1 5.7 33993 12.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.36 1.43 37.8 0.69 0.86 0.51 0.54 1.1 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.36 45.96 33976 1690 80.909 0.168 0.1667 0.175 0.193 0.1943 17.896
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] 1.056 0.03 -1.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.613 r_dihedral_angle_6_deg 17.133 r_dihedral_angle_3_deg 11.575 r_lrange_it 10.28 r_lrange_other 10.277 r_dihedral_angle_other_2_deg 7.728 r_dihedral_angle_1_deg 6.439 r_scangle_it 6.311 r_scangle_other 6.309 r_scbond_it 4.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.613 r_dihedral_angle_6_deg 17.133 r_dihedral_angle_3_deg 11.575 r_lrange_it 10.28 r_lrange_other 10.277 r_dihedral_angle_other_2_deg 7.728 r_dihedral_angle_1_deg 6.439 r_scangle_it 6.311 r_scangle_other 6.309 r_scbond_it 4.357 r_scbond_other 4.354 r_mcangle_it 4.316 r_mcangle_other 4.316 r_rigid_bond_restr 3.704 r_mcbond_it 2.877 r_mcbond_other 2.875 r_angle_refined_deg 2.068 r_angle_other_deg 1.293 r_symmetry_nbd_refined 0.299 r_nbd_refined 0.189 r_nbtor_refined 0.155 r_symmetry_nbd_other 0.124 r_chiral_restr 0.118 r_nbd_other 0.084 r_symmetry_xyhbond_nbd_refined 0.081 r_xyhbond_nbd_refined 0.069 r_symmetry_nbtor_other 0.064 r_gen_planes_refined 0.018 r_bond_refined_d 0.012 r_bond_other_d 0.008 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1350 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing