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Crystal Structure of KRasG13C in Complex with Nucleotide-based Covalent Inhibitor 7b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OK3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 30 % PEG4000, 100 mM NaAc pH 9.0, 200 mM Tris pH 9.0
followed by shrinking of the crystal in new drop with crytallization condition, SEC buffer and 20 % glycerol for 24 h.
Crystal Properties Matthews coefficient Solvent content 2.07 40.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.01 α = 90 b = 84.76 β = 113.254 c = 88.77 γ = 90
Symmetry Space Group C 1 2 1
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 2024-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.85 50 99.8 0.046 0.999 18.37 6.86 40664 44.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 99.7 1.269 0.618 1.37 6.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.85 42.38 1.36 40651 2034 99.93 0.1917 0.1898 0.1897 0.2278 0.2276 59.43
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.7933 f_angle_d 1.2494 f_chiral_restr 0.0793 f_bond_d 0.011 f_plane_restr 0.0084
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3625 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 126
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement Coot model building