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Crystal structure of human KRAS G12C covalently bound to DEL triazine 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 6.5 293 0.001M calcium chloride, 0.1M MES pH6.5, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.94 36.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.715 α = 90 b = 40.715 β = 90 c = 341.304 γ = 120
Symmetry Space Group P 65 2 2
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 EIGER X 16M 2020-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00000 APS 22-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 1.65 30 91.9 0.048 0.998 12.34 3.5 34847
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 1.65 1.75 68.5 0.461 0.861 1.96 3.4
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 1.65 30 18826 955 91.27 0.21066 0.20871 0.2192 0.24989 0.2545 RANDOM 35.819
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] 1.12 0.56 1.12 -3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.658 r_dihedral_angle_4_deg 20.116 r_dihedral_angle_3_deg 13.711 r_dihedral_angle_1_deg 4.775 r_long_range_B_refined 4.438 r_long_range_B_other 4.397 r_scangle_other 2.923 r_mcangle_it 2.268 r_mcangle_other 2.267 r_scbond_it 1.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.658 r_dihedral_angle_4_deg 20.116 r_dihedral_angle_3_deg 13.711 r_dihedral_angle_1_deg 4.775 r_long_range_B_refined 4.438 r_long_range_B_other 4.397 r_scangle_other 2.923 r_mcangle_it 2.268 r_mcangle_other 2.267 r_scbond_it 1.748 r_scbond_other 1.747 r_mcbond_it 1.382 r_mcbond_other 1.376 r_angle_refined_deg 1.176 r_angle_other_deg 0.679 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.001 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 1351 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 70
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing REFMAC refinement Coot model building