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Crystal structure of unbound N-SH2 domain of SHP2
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;
500 nL of 1.0 M sodium malonate pH 5.0, 0.1 M sodium acetate trihydrate pH 4.5, and 2% w/v polyethylene glycol 20,000
Crystal Properties Matthews coefficient Solvent content 2.93 58.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.464 α = 90 b = 60.464 β = 90 c = 78.293 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 PILATUS3 6M 2021-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0004 ALS 5.0.2
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 1.83 42.75 99.49 1 26 15 13292 49.86
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 1.83 1.9 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 1.83 42.75 1.33 13291 1328 99.48 0.2322 0.2295 0.2358 0.2549 0.2602 64.69
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 20.3255 f_angle_d 0.8134 f_chiral_restr 0.0516 f_plane_restr 0.0066 f_bond_d 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 811 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing Coot model building