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RAS GUANINE EXCHANGE FACTOR SOS1 (REM-CDC25) IN COMPLEX WITH KRAS(G12C) AND FRAGMENT SCREENING HIT F4
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 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 three days at 277 K 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 3.68 66.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.98 α = 90 b = 149.98 β = 90 c = 200.37 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-F 2014-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 47.43 99.9 0.113 0.998 17.4 9.5 44844 47.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.54 99.9 0.845 0.895 2.5 9.7
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 2.4 47.43 42657 2165 99.93 0.17843 0.17728 0.20076 0.2004 RANDOM 53.999
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] -0.51 -0.51 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.531 r_dihedral_angle_3_deg 17.97 r_dihedral_angle_4_deg 17.596 r_long_range_B_refined 11.066 r_long_range_B_other 11.064 r_scangle_other 7.216 r_dihedral_angle_1_deg 5.723 r_mcangle_it 5.576 r_mcangle_other 5.576 r_scbond_it 4.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.531 r_dihedral_angle_3_deg 17.97 r_dihedral_angle_4_deg 17.596 r_long_range_B_refined 11.066 r_long_range_B_other 11.064 r_scangle_other 7.216 r_dihedral_angle_1_deg 5.723 r_mcangle_it 5.576 r_mcangle_other 5.576 r_scbond_it 4.502 r_scbond_other 4.501 r_mcbond_it 3.435 r_mcbond_other 3.431 r_angle_refined_deg 1.517 r_angle_other_deg 1.011 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 5163 Nucleic Acid Atoms Solvent Atoms 299 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing