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Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with KRAS(G12C) and fragment screening hit F1
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 one day 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 = 150.223 α = 90 b = 150.223 β = 90 c = 200.471 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 2014-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 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 48.6 99.5 0.111 0.118 0.999 17.5 8.8 39718 50.5
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 97.1 0.943 1 0.771 2.4 8.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1BKD 2.5 48.58 37731 1986 99.46 0.1813 0.17974 0.21088 0.1829 RANDOM 55.725
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] 0.08 0.08 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.359 r_dihedral_angle_3_deg 16.472 r_dihedral_angle_4_deg 14.046 r_long_range_B_refined 10.012 r_long_range_B_other 10.011 r_scangle_other 7.116 r_mcangle_it 6.101 r_mcangle_other 6.101 r_dihedral_angle_1_deg 5.777 r_scbond_it 4.478
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.359 r_dihedral_angle_3_deg 16.472 r_dihedral_angle_4_deg 14.046 r_long_range_B_refined 10.012 r_long_range_B_other 10.011 r_scangle_other 7.116 r_mcangle_it 6.101 r_mcangle_other 6.101 r_dihedral_angle_1_deg 5.777 r_scbond_it 4.478 r_scbond_other 4.477 r_mcbond_it 3.781 r_mcbond_other 3.762 r_angle_refined_deg 1.323 r_angle_other_deg 0.959 r_chiral_restr 0.079 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 230 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing