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CRYSTAL STRUCTURE OF INACTIVE KRAS G12D (GDP) IN COMPLEX WITH THE SOAKED DIMERIC INHIBITOR BI-5747
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 278 200 mM CaCl2
100 mM MES pH6
PEG6000 20% W/v
Crystal Properties Matthews coefficient Solvent content 2.38 48.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.883 α = 90 b = 66.316 β = 95.12 c = 74.537 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 16M 2016-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.857 74 91.6 0.072 0.098 0.052 1 10.5 3.5 43278
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.858 1.863 0.8
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 FREE R-VALUE 6QUU 1.86 37.12 1.37 43017 2192 91.5 0.1755 0.1737 0.174 0.2097 0.2104
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 15.527 f_angle_d 1.128 f_chiral_restr 0.321 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3864 Nucleic Acid Atoms Solvent Atoms 485 Heterogen Atoms 187
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling BUSTER phasing