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Crystal Structure of wild-type KRAS (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF (crystal form II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VJJ 6VJJ, 1FAR experimental model PDB 1FAR 6VJJ, 1FAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM sodium cacodylate pH 6.5, 200 mM sodium citrate, 15% 2-propanol, 0.25% (w/v) n-octyl-beta-D-glucoside, 0.35 mM D-myo-phosphatidylinositol 3,4,5-triphosphate, and 0.25% (w/v) n-dodecyl-beta-D-maltoside
Crystal Properties Matthews coefficient Solvent content 3.27 62.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.984 α = 90 b = 133.984 β = 90 c = 89.275 γ = 120
Symmetry Space Group P 6 2 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 2018-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9791 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 48.65 98.4 0.089 0.097 0.999 14.03 6.164 16642 59.192
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 99.2 0.86 0.937 0.74 1.91 6.265
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6VJJ, 1FAR 2.5 48.65 1.34 16638 1664 98.39 0.19 0.1863 0.1905 0.2213 0.2236 62.1845
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2402 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 54
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement