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Crystal structure of human KRAS G12C covalently bound to thiazol-2-yl piperidine compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 500mM lithium chloride, 100mM TRIS, 30% PEG 6000, 100mM sodium/potassium tartrate
Crystal Properties Matthews coefficient Solvent content 2.41 49.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.777 α = 90 b = 93.777 β = 90 c = 120.471 γ = 120
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 2024-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00000 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 50 99.6 0.067 0.999 13.12 5.06 69153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.54 99.1 1.308 0.452 1.15 4.95
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 1.45 30 34006 1791 99.6 0.18046 0.17993 0.1848 0.18994 0.1934 RANDOM 21.759
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] -0.14 -0.07 -0.14 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.015 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_1_deg 5.85 r_long_range_B_refined 4.598 r_long_range_B_other 4.413 r_scangle_other 2.942 r_mcangle_it 2.145 r_mcangle_other 2.145 r_scbond_it 1.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.015 r_dihedral_angle_4_deg 16.89 r_dihedral_angle_3_deg 13.534 r_dihedral_angle_1_deg 5.85 r_long_range_B_refined 4.598 r_long_range_B_other 4.413 r_scangle_other 2.942 r_mcangle_it 2.145 r_mcangle_other 2.145 r_scbond_it 1.828 r_scbond_other 1.827 r_angle_refined_deg 1.476 r_angle_other_deg 1.325 r_mcbond_it 1.315 r_mcbond_other 1.31 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1352 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction