☰ Navigation Tabs
Co-crystal Structure of KRAS (G12C) covalently bound with Quinazoline based inhibitor JBI739
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 0.01M tri-Sodium citrate, 33% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.41 48.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.391 α = 90 b = 51.73 β = 90 c = 89.242 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 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 1.69 50 96.2 0.092 0.046 15.7 4.8 21722
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 1.69 1.76 0.359 0.234
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 1.69 44.77 19773 1067 96.98 0.19918 0.1974 0.2063 0.23482 0.2452 RANDOM 24.813
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] 0.54 -0.28 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.029 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 4.864 r_scangle_it 1.931 r_scbond_it 1.277 r_angle_refined_deg 1.222 r_mcangle_it 0.93 r_angle_other_deg 0.709 r_mcbond_it 0.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.029 r_dihedral_angle_4_deg 16.814 r_dihedral_angle_3_deg 13.431 r_dihedral_angle_1_deg 4.864 r_scangle_it 1.931 r_scbond_it 1.277 r_angle_refined_deg 1.222 r_mcangle_it 0.93 r_angle_other_deg 0.709 r_mcbond_it 0.628 r_nbd_refined 0.2 r_nbtor_refined 0.191 r_symmetry_vdw_other 0.191 r_nbd_other 0.188 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.131 r_mcbond_other 0.101 r_symmetry_vdw_refined 0.099 r_nbtor_other 0.079 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 1348 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing