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Co-crystal structure of SOS-1 and a potent, selective and orally bioavailable SOS1 inhibitor RGT-018
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1 M imidazole 8.0, 6% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.25 45.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.76 α = 90 b = 83.85 β = 90 c = 179.02 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 XE 16M 2020-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.98 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 44.8 99.95 1 26.38 2 36854
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 2.1 2.175 0.927
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 MOLECULAR REPLACEMENT THROUGHOUT 5OVE 2.1 44.8 34998 1855 99.97 0.22202 0.21976 0.2281 0.26389 0.2705 RANDOM 59.841
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] 5.68 -4.69 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.351 r_dihedral_angle_4_deg 20.843 r_dihedral_angle_3_deg 17.273 r_long_range_B_other 9.446 r_long_range_B_refined 9.445 r_scangle_other 7.346 r_mcangle_other 6.904 r_mcangle_it 6.899 r_dihedral_angle_1_deg 6.759 r_scbond_it 5.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.351 r_dihedral_angle_4_deg 20.843 r_dihedral_angle_3_deg 17.273 r_long_range_B_other 9.446 r_long_range_B_refined 9.445 r_scangle_other 7.346 r_mcangle_other 6.904 r_mcangle_it 6.899 r_dihedral_angle_1_deg 6.759 r_scbond_it 5.271 r_scbond_other 5.27 r_mcbond_it 5.103 r_mcbond_other 5.091 r_angle_refined_deg 1.558 r_angle_other_deg 1.264 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 3920 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing