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Crystal structure of human KRAS-G12C covalent bound to Olomorasib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 100mM Tris HCl pH 7.5 + 26.7% PEG 4K + 200mM Calcium Chloride
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.503 α = 90 b = 39.464 β = 96.81 c = 53.222 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 6M 2020-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.11 30 75.8 0.075 14.9 6.6 49674
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.11 1.14 0.599
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 1.11 30 49674 2557 75.64 0.16415 0.16288 0.1682 0.18936 0.1921 RANDOM 13.07
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] 0.3 -0.12 -0.01 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.243 r_dihedral_angle_1_deg 5.253 r_dihedral_angle_2_deg 5.079 r_scbond_it 4.139 r_rigid_bond_restr 3.274 r_long_range_B_refined 3.12 r_mcangle_it 1.769 r_mcbond_it 1.664 r_angle_refined_deg 1.264 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.243 r_dihedral_angle_1_deg 5.253 r_dihedral_angle_2_deg 5.079 r_scbond_it 4.139 r_rigid_bond_restr 3.274 r_long_range_B_refined 3.12 r_mcangle_it 1.769 r_mcbond_it 1.664 r_angle_refined_deg 1.264 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1308 Nucleic Acid Atoms 41 Solvent Atoms 100 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing