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Crystal structure of KRAS-G12C in complex with compound 16 (JAB-16)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6P8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.3 277 0.2 M Magnesium Chloride, 0.1 M Tris pH 8.3, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.39 43.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.69 α = 90 b = 86.69 β = 90 c = 42.68 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 EIGER X 9M 2020-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12713 APS 21-ID-D
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 1.41 43.383 99.7 0.075 0.999 25.1 13.6 35392
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 1.41 1.43 0.716 0.766 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.41 43.383 35329 1796 99.555 0.18 0.1792 0.1792 0.1936 0.194 12.698
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] -0.266 -0.133 -0.266 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.274 r_dihedral_angle_4_deg 13.372 r_dihedral_angle_3_deg 11.184 r_dihedral_angle_1_deg 6.548 r_lrange_it 3.924 r_lrange_other 3.767 r_scangle_it 1.776 r_scangle_other 1.775 r_angle_refined_deg 1.438 r_mcangle_it 1.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.274 r_dihedral_angle_4_deg 13.372 r_dihedral_angle_3_deg 11.184 r_dihedral_angle_1_deg 6.548 r_lrange_it 3.924 r_lrange_other 3.767 r_scangle_it 1.776 r_scangle_other 1.775 r_angle_refined_deg 1.438 r_mcangle_it 1.417 r_mcangle_other 1.417 r_angle_other_deg 1.37 r_scbond_other 1.112 r_scbond_it 1.111 r_mcbond_it 0.819 r_mcbond_other 0.816 r_nbd_refined 0.21 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.165 r_nbd_other 0.14 r_xyhbond_nbd_refined 0.125 r_symmetry_nbd_refined 0.096 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1349 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing