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Crystal structure of KRAS G13C (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of BRAF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.8 M sodium acetate and 0.1 M Bis-Tris propane, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.76 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.788 α = 90 b = 166.788 β = 90 c = 166.788 γ = 90
Symmetry Space Group I 4 3 2
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 16M 2019-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.85 52.74 100 0.11 0.044 0.999 13.5 7.2 17527
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 100 2.017 0.816 0.316 7
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 2.85 52.74 0.01 17525 927 99.97 0.2115 0.2096 0.2282 0.2443 0.2442
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 19.45 f_angle_d 0.642 f_chiral_restr 0.044 f_plane_restr 0.01 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2395 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing