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Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor compound 1
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, HANGING DROP 293 Protein concentration 30.7 mg/ml. Protein buffer 25 Millimolar TRIS-HCL PH 7.5, 50 millimolar NaCl, 1 millimolar DTT. Reservoir 25% (v/v) ethylenglycol. Protein incubated with 2 MILLIMOLAR LIGAND prior to crystallization.
Crystal Properties Matthews coefficient Solvent content 2.72 54.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.335 α = 90 b = 85.26 β = 90 c = 176.976 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-F 2017-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
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 1.85 48.51 99.6 0.06 0.998 15.55 6.5 54441 41.75
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 1.85 1.96 98.5 0.806 0.606 1.86 6.8
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 2ii0 1.85 48.51 52340 2100 99.6 0.2754 0.27346 0.2776 0.32307 0.3234 RANDOM 49.407
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] 4.05 -2.41 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.887 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_4_deg 11.243 r_long_range_B_refined 6.883 r_long_range_B_other 6.883 r_dihedral_angle_1_deg 4.526 r_scangle_other 4.464 r_mcangle_it 4.284 r_mcangle_other 4.283 r_mcbond_it 2.768
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.887 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_4_deg 11.243 r_long_range_B_refined 6.883 r_long_range_B_other 6.883 r_dihedral_angle_1_deg 4.526 r_scangle_other 4.464 r_mcangle_it 4.284 r_mcangle_other 4.283 r_mcbond_it 2.768 r_mcbond_other 2.767 r_scbond_it 2.727 r_scbond_other 2.726 r_angle_refined_deg 1.04 r_angle_other_deg 0.86 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 329 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing