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Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide (624-633) QVEpYLDLDLD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 500 nL of 10 mg/mL SHP2 N-SH2 in 50 mM Bis-Tris pH 6.5, 50 mM NaCl, 1 mM TCEP, with GAB1 (QVEpYLDLDLD) 1:1.05 molar ratio;
500 nL of 6% v/v Tacsimate pH 6.0,
0.1 M MES monohydrate pH 6.0, and 25% w/v polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.53 α = 90 b = 61.53 β = 90 c = 73.445 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 CCD ADSC QUANTUM 315r 2021-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0005 ALS 8.2.1
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 1.59 37.43 99.94 1 15.98 25.9 19583 34.77
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 1.59 1.63 99.85 0.415 27.1
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 1.59 37.43 1.33 19571 1956 99.94 0.2046 0.2009 0.2002 0.24 0.2391 51.88
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 18.2653 f_angle_d 1.2779 f_chiral_restr 0.0571 f_plane_restr 0.0123 f_bond_d 0.0101
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 890 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing Coot model building