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Co-crystal Structure of KRAS (G12C) covalently bound with Quinazoline based inhibitor JBI484
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F2E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.15M K Bromide, 30% w/v PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 1.97 37.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.604 α = 90 b = 53.089 β = 90 c = 69.106 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE MAR scanner 345 mm plate Varimax HR 2017-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.7 50 96.2 0.099 0.048 14.8 4.7 17506
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 0.349 0.214
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5F2E 1.7 42.11 15943 860 97.16 0.20186 0.20011 0.1979 0.23692 0.2339 RANDOM 21.135
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] -0.43 0.61 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.923 r_dihedral_angle_3_deg 13.171 r_dihedral_angle_4_deg 11.733 r_dihedral_angle_1_deg 4.996 r_scangle_it 1.818 r_scbond_it 1.188 r_angle_refined_deg 1.18 r_mcangle_it 0.858 r_mcbond_it 0.513 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.923 r_dihedral_angle_3_deg 13.171 r_dihedral_angle_4_deg 11.733 r_dihedral_angle_1_deg 4.996 r_scangle_it 1.818 r_scbond_it 1.188 r_angle_refined_deg 1.18 r_mcangle_it 0.858 r_mcbond_it 0.513 r_nbtor_refined 0.305 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.176 r_xyhbond_nbd_refined 0.11 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1339 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing