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Structure of the N-SH2 domain of SHP2 in complex with the phosphoY627-Gab1 (613-651) peptide
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, HANGING DROP 293 5 % PEG3350, 0.2 M NaCl, 0.1 M BisTris, pH 5.5
Crystal Properties Matthews coefficient Solvent content 1.99 38.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.78 α = 90 b = 60.78 β = 90 c = 69.847 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 RIGAKU HyPix-Arc 150 2021-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.08 69.85 100 0.137 0.998 14 14.2 8364 31.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.14 100 0.95 0.817 2.9 13.3
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 2.08 27.87 1.34 8295 405 99.7 0.2281 0.2258 0.2254 0.2729 0.2718 36.2
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 15.794 f_angle_d 0.9502 f_chiral_restr 0.0499 f_plane_restr 0.0071 f_bond_d 0.0061
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 870 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing