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Crystal structure of human KRAS G12C covalently bound to 4-methyl-thiazol-5-yl piperidine compound 4
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 200mM lithium sulfate, 100mM TRIS, 30% PEG 4000, 5mM magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.699 α = 90 b = 93.699 β = 90 c = 120.826 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 1.1 50 99.4 0.05 0.999 14.02 4.83 158273
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 1.1 1.17 96.5 1.144 0.522 1.13 3.88
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 1.1 30 77467 4007 99.64 0.18013 0.17958 0.1895 0.19054 0.1997 RANDOM 14.785
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] -0.19 -0.1 -0.19 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_4_deg 18.014 r_dihedral_angle_3_deg 11.647 r_dihedral_angle_1_deg 5.711 r_long_range_B_refined 3.67 r_long_range_B_other 3.37 r_angle_other_deg 1.574 r_scangle_other 1.571 r_angle_refined_deg 1.478 r_mcangle_it 1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_4_deg 18.014 r_dihedral_angle_3_deg 11.647 r_dihedral_angle_1_deg 5.711 r_long_range_B_refined 3.67 r_long_range_B_other 3.37 r_angle_other_deg 1.574 r_scangle_other 1.571 r_angle_refined_deg 1.478 r_mcangle_it 1.315 r_mcangle_other 1.314 r_scbond_it 0.964 r_scbond_other 0.963 r_mcbond_it 0.767 r_mcbond_other 0.764 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.005 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 188 Heterogen Atoms 69
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction