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Ras guanine nucleotide exchange factor SOS1 (Rem-cdc25) in complex with small molecule inhibitor compound 21
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 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 23% (v/v) ethylenglycol. Protein incubated with 5 MILLIMOLAR LIGAND overnight at 277K prior to crystallization.
Crystal Properties Matthews coefficient Solvent content 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.413 α = 90 b = 85.362 β = 90 c = 176.221 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 2015-08-20 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 2.3 48.4 99.5 0.051 0.999 22.13 5.3 28560 45.4
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 2.3 2.44 98.8 0.328 0.94 4.86 5.33
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 2ii0 2.3 44.06 27149 1429 99.59 0.26324 0.25969 0.2605 0.33022 0.3333 RANDOM 49.569
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] 3.86 -1.98 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.787 r_dihedral_angle_3_deg 14.43 r_dihedral_angle_4_deg 11.681 r_long_range_B_refined 7.712 r_long_range_B_other 7.711 r_scangle_other 5.229 r_mcangle_it 5.123 r_mcangle_other 5.122 r_dihedral_angle_1_deg 4.828 r_mcbond_it 3.229
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.787 r_dihedral_angle_3_deg 14.43 r_dihedral_angle_4_deg 11.681 r_long_range_B_refined 7.712 r_long_range_B_other 7.711 r_scangle_other 5.229 r_mcangle_it 5.123 r_mcangle_other 5.122 r_dihedral_angle_1_deg 4.828 r_mcbond_it 3.229 r_mcbond_other 3.223 r_scbond_it 3.17 r_scbond_other 3.167 r_angle_refined_deg 1.098 r_angle_other_deg 0.863 r_chiral_restr 0.058 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 3778 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing