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Crystal structure of N-SH2 domain of SHP2 bound to phosphotyrosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 10 mg/mL WT N-SH2 with 20 mM O-phospho-L-tyrosine in 0.5 M Tris pH 9.0,
100 mM sodium acetate pH 4.6, and 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.86 56.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.596 α = 90 b = 58.596 β = 90 c = 81.269 γ = 90
Symmetry Space Group P 43 21 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 2022-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
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 1.71 36.91 99.86 1 9.4 15 15891 34.5
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 1.71 1.77 99.08 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.71 33.39 1.33 15890 1589 99.86 0.2081 0.2039 0.2042 0.2461 0.247 43.24
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 13.5057 f_angle_d 1.0055 f_chiral_restr 0.0745 f_bond_d 0.013 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 828 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building