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Crystal structure of KRAS-G12C in complex with Compound 20 (JAB-20)
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 5.3 277 0.1 M Sodium cacodylate, pH 5.3, 25% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.92 29.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.44 α = 90 b = 78.6 β = 90 c = 109.58 γ = 90
Symmetry Space Group P 2 21 21
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 2020-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
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 1.29 44.954 99.9 0.182 0.987 11 11.7 75841
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 1.29 1.31 0.222 0.962 5.4
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.29 44.954 75770 3733 99.816 0.174 0.1726 0.1931 0.2343 10.434
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] -0.345 -0.111 0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_4_deg 19.989 r_dihedral_angle_3_deg 12.247 r_dihedral_angle_1_deg 5.926 r_lrange_it 4.182 r_lrange_other 4.032 r_angle_refined_deg 1.516 r_scangle_it 1.494 r_scangle_other 1.493 r_angle_other_deg 1.398
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_4_deg 19.989 r_dihedral_angle_3_deg 12.247 r_dihedral_angle_1_deg 5.926 r_lrange_it 4.182 r_lrange_other 4.032 r_angle_refined_deg 1.516 r_scangle_it 1.494 r_scangle_other 1.493 r_angle_other_deg 1.398 r_mcangle_it 1.114 r_mcangle_other 1.114 r_scbond_it 0.925 r_scbond_other 0.923 r_mcbond_it 0.66 r_mcbond_other 0.66 r_symmetry_nbd_refined 0.248 r_nbd_other 0.219 r_symmetry_xyhbond_nbd_other 0.218 r_nbd_refined 0.212 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.159 r_ncsr_local_group_1 0.143 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.064 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing