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Structure of human SHP2 without N-SH2 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DGP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 100 mM ammonium formate, 22% PEG 3,350 and 1.5% xylitol
Crystal Properties Matthews coefficient Solvent content 2.64 53.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.55 α = 90 b = 56.2 β = 93.99 c = 247.46 γ = 90
Symmetry Space Group P 1 21 1
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 315 2016-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9999 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.9 82.29 99.2 0.5172 4.3 4.6 42597 41.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.01 99.4 0.7646 4.7
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 4dgp 2.9 82.29 1.35 42398 1997 98.54 0.2504 0.2491 0.2486 0.2764 0.2749 48.8
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 7.1042 f_angle_d 0.4447 f_chiral_restr 0.0415 f_plane_restr 0.0029 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12505 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection iMOSFLM data reduction Aimless data scaling PHASER phasing Coot model building PHENIX refinement