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Crystal structure of SOS1-HRas-peptidomimetic3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 sodium formate 3 M, Tris 100mM pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.24 62.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.05 α = 90 b = 143.05 β = 90 c = 208.33 γ = 90
Symmetry Space Group I 4 2 2
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 EIGER X 16M 2019-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565037 SOLEIL PROXIMA 1
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 3 47.0513233812 99.8 0.99 18.9 26.7 21977 96.69
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 3 3.18 0.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1BKD 3 47.05 1.35 21959 1098 99.77 0.2257 0.2235 0.224 0.2665 0.2667 95.42
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.0204 f_angle_d 0.9676 f_chiral_restr 0.0515 f_plane_restr 0.0071 f_bond_d 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4978 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 77
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing