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Crystal structure of human KRAS G12C covalently bound to 1,4-dimethyl-pyrazol-5-yl piperidine compound 5
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 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.188 α = 90 b = 94.188 β = 90 c = 122.012 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 EIGER2 XE 9M 2024-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97856 NSLS-II 19-ID
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 1.26 50 97.2 0.142 0.987 8.39 5.88 105547
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 1.26 1.34 86.7 0.822 0.637 1.81 2.85
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 1.26 30 52341 2647 98.33 0.1933 0.19261 0.1937 0.20645 0.2076 RANDOM 18.467
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] -0.22 -0.11 -0.22 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.925 r_dihedral_angle_4_deg 21.256 r_dihedral_angle_3_deg 11.993 r_dihedral_angle_1_deg 6.019 r_long_range_B_refined 3.927 r_long_range_B_other 3.649 r_scangle_other 2.212 r_mcangle_it 1.619 r_mcangle_other 1.619 r_angle_refined_deg 1.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.925 r_dihedral_angle_4_deg 21.256 r_dihedral_angle_3_deg 11.993 r_dihedral_angle_1_deg 6.019 r_long_range_B_refined 3.927 r_long_range_B_other 3.649 r_scangle_other 2.212 r_mcangle_it 1.619 r_mcangle_other 1.619 r_angle_refined_deg 1.447 r_angle_other_deg 1.435 r_scbond_it 1.38 r_scbond_other 1.379 r_mcbond_it 0.976 r_mcbond_other 0.972 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 170 Heterogen Atoms 70
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction