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Crystal Structure of a G12C Oncogenic Variant of Human KRas Bound to a Novel GDP Competitive Covalent Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EPV PDB ENTRY 4EPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 277 0.2M MMT pH4.0, 28% PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.93 36.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.088 α = 90 b = 42.022 β = 90 c = 91.159 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 CCD ADSC QUANTUM 315 2013-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.89 50 99.8 0.126 14.469 5.8 12363 2 23.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.883 2.036 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 4EPV 1.89 45.58 12363 11695 615 0.186 0.184 0.1921 0.237 0.2433 RANDOM 25.81
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] -2.46 3.17 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_4_deg 20.314 r_dihedral_angle_3_deg 12.006 r_long_range_B_refined 6.816 r_long_range_B_other 6.723 r_scangle_other 5.14 r_dihedral_angle_1_deg 5.011 r_scbond_other 3.259 r_scbond_it 3.257 r_mcangle_other 2.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_4_deg 20.314 r_dihedral_angle_3_deg 12.006 r_long_range_B_refined 6.816 r_long_range_B_other 6.723 r_scangle_other 5.14 r_dihedral_angle_1_deg 5.011 r_scbond_other 3.259 r_scbond_it 3.257 r_mcangle_other 2.974 r_mcangle_it 2.963 r_mcbond_it 2.152 r_mcbond_other 2.108 r_angle_refined_deg 1.364 r_angle_other_deg 0.768 r_chiral_restr 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.004 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1357 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 35
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling