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Ras guanine exchange factor SOS1 (Rem-cdc25) in complex with KRAS(G12C) and fragment screening hit F2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 Drops made from KRAS SOS1 complex (14.4 mg/ml in 5 mM Tris pH 7.5, 100mM NaCl) and reservoir solution (2.9 to 3.4 M sodium formate, 100 mM MES pH 6.5). Fragment soaked at 25 mM for 2.5 days using a 500 mM fragment stock solution in DMSO. Cryo buffer 0.1 M MES pH 6.5, 3.5 M sodium formate, 20 glycerol, 25 mM fragment.
Crystal Properties Matthews coefficient Solvent content 3.7 66.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.99 α = 90 b = 149.99 β = 90 c = 201.07 γ = 90
Symmetry Space Group I 4 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 2014-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 48.5 98.6 0.118 0.125 0.998 15.5 9 39446
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 98.3 0.862 0.912 0.751 2.6 9.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1BKD 2.5 47.41 37472 1973 98.61 0.17916 0.17716 0.1826 0.2185 0.2233 RANDOM 53.29
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] -0.12 -0.12 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.27 r_dihedral_angle_3_deg 16.705 r_dihedral_angle_4_deg 16.08 r_long_range_B_refined 10.388 r_long_range_B_other 10.388 r_scangle_other 7.833 r_mcangle_it 6.561 r_mcangle_other 6.561 r_dihedral_angle_1_deg 6.049 r_scbond_it 4.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.27 r_dihedral_angle_3_deg 16.705 r_dihedral_angle_4_deg 16.08 r_long_range_B_refined 10.388 r_long_range_B_other 10.388 r_scangle_other 7.833 r_mcangle_it 6.561 r_mcangle_other 6.561 r_dihedral_angle_1_deg 6.049 r_scbond_it 4.925 r_scbond_other 4.924 r_mcbond_it 4.101 r_mcbond_other 4.095 r_angle_refined_deg 1.359 r_angle_other_deg 0.968 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5193 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing