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Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor BAY-293 (compound 23)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2II0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Protein concentration 30.7 mg/ml. Protein buffer 25 Millimolar TRIS-HCL PH 7.5, 50 millimolar NaCl, 1 millimolar DTT. Reservoir 0.1 M TRIS pH 8.5, 25 % (w/v) PEG 3350. CRYO BUFFER WAS RESERVOIR SUPPLEMENTED WITH 2 MILLIMOLAR INHIBITOR (FROM 100 MILLIMOLAR DMSO STOCK) AND 15 % (v/v) ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.476 α = 90 b = 84.281 β = 90 c = 175.285 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 PILATUS 6M 2017-03-02 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 2.2 48.02 98.5 0.14 0.984 5.75 3.71 112189 30220 41.9
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 2.2 2.33 99.5 0.644 0.674 1.54 3.79
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 MOLECULAR REPLACEMENT THROUGHOUT 2ii0 2.2 48.02 28708 1511 98.54 0.21255 0.21062 0.24932 0.2433 RANDOM 42.192
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] 1.69 -2.09 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.167 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_4_deg 14.019 r_long_range_B_refined 5.76 r_long_range_B_other 5.759 r_dihedral_angle_1_deg 4.94 r_scangle_other 2.971 r_mcangle_it 2.574 r_mcangle_other 2.574 r_scbond_it 1.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.167 r_dihedral_angle_3_deg 14.532 r_dihedral_angle_4_deg 14.019 r_long_range_B_refined 5.76 r_long_range_B_other 5.759 r_dihedral_angle_1_deg 4.94 r_scangle_other 2.971 r_mcangle_it 2.574 r_mcangle_other 2.574 r_scbond_it 1.727 r_scbond_other 1.727 r_mcbond_other 1.495 r_mcbond_it 1.494 r_angle_refined_deg 1.12 r_angle_other_deg 0.882 r_chiral_restr 0.061 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 3870 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing