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Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor compound 17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other INHOUSE STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein concentration 30.7 mg/ml. Protein buffer 25 Millimolar TRIS-HCL PH 7.5, 50 millimolar NaCl, 1 millimolar DTT. Reservoir 27% (v/v) ethylenglycol. Protein incubated with 2 MILLIMOLAR LIGAND prior to crystallization.
Crystal Properties Matthews coefficient Solvent content 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.895 α = 90 b = 85.161 β = 90 c = 176.537 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 PILATUS3 S 6M 2015-06-25 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) 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 2.01 48.41 99.3 0.112 0.998 10.83 4.36 40982 35.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.01 2.13 98.3 0.79 0.665 1.87 4.33
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 INHOUSE STRUCTURE 2.01 48.41 38932 2050 99.3 0.24829 0.24635 0.2501 0.28501 0.2886 RANDOM 35.94
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] 3.49 -2.35 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.959 r_dihedral_angle_4_deg 15.743 r_dihedral_angle_3_deg 13.714 r_long_range_B_refined 6.135 r_long_range_B_other 6.135 r_dihedral_angle_1_deg 4.663 r_scangle_other 3.74 r_mcangle_it 3.167 r_mcangle_other 3.167 r_scbond_it 2.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.959 r_dihedral_angle_4_deg 15.743 r_dihedral_angle_3_deg 13.714 r_long_range_B_refined 6.135 r_long_range_B_other 6.135 r_dihedral_angle_1_deg 4.663 r_scangle_other 3.74 r_mcangle_it 3.167 r_mcangle_other 3.167 r_scbond_it 2.204 r_scbond_other 2.203 r_mcbond_it 1.956 r_mcbond_other 1.956 r_angle_refined_deg 1.042 r_angle_other_deg 0.863 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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 3910 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing