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Crystal Structure of human KRAS G12C covalently bound to nopinone-derived naphthol compound 21
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 5.6 293 0.2M ammonium acetate, 0.1M sodium citrate pH5.6, 32% PEG4000, 0.005M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.386 α = 90 b = 39.854 β = 100.38 c = 52.718 γ = 90
Symmetry Space Group P 1 21 1
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 2024-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00003 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 1.18 50 93.9 0.056 0.995 10.24 2.6 111983
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 1.18 1.25 79.1 0.208 0.925 2.85 2.1
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 1.18 30 55366 2803 95.45 0.17828 0.17724 0.1861 0.19863 0.1974 RANDOM 14.673
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] 0.44 0.03 -0.02 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.273 r_dihedral_angle_4_deg 21.082 r_dihedral_angle_3_deg 11.513 r_dihedral_angle_1_deg 6.163 r_long_range_B_refined 3.428 r_long_range_B_other 3.201 r_scangle_other 1.491 r_angle_refined_deg 1.392 r_angle_other_deg 1.304 r_mcangle_it 1.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.273 r_dihedral_angle_4_deg 21.082 r_dihedral_angle_3_deg 11.513 r_dihedral_angle_1_deg 6.163 r_long_range_B_refined 3.428 r_long_range_B_other 3.201 r_scangle_other 1.491 r_angle_refined_deg 1.392 r_angle_other_deg 1.304 r_mcangle_it 1.252 r_mcangle_other 1.251 r_scbond_it 0.929 r_scbond_other 0.929 r_mcbond_it 0.722 r_mcbond_other 0.718 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 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 1342 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 78
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement Coot model building