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Crystal Structure of KRAS-G12V (GMPPNP-bound) in complex with RAS-binding domain (RBD) and cysteine-rich domain (CRD) of RAF1/CRAF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other KRAS:RAF1-RBDCRD (crystal form II)
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 MgCl2, 8% PGA, 0.35 mM D-myo-phosphatidylinositol 3,4,5-triphosphate
Crystal Properties Matthews coefficient Solvent content 3.23 61.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.1 α = 90 b = 132.1 β = 90 c = 90.17 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 PILATUS 6M-F 2018-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9791 APS 24-ID-C
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 2.87 48.3 98.5 0.071 0.079 0.998 16.04 5.8 10931 82.28
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 2.87 2.97 99.7 0.885 0.965 0.827 2.53 6.2
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 KRAS:RAF1-RBDCRD (crystal form II) 2.87 48.3 1.37 10930 1093 98.56 0.2219 0.2167 0.2227 0.2691 0.2709 102.9443
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 2386 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 61
Software Software Software Name Purpose XDS data reduction SCALA data scaling PHASER phasing PHENIX refinement