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Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TNO155
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2SHP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 17% PEG 3350 and 200 mM ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 2.45 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.292 α = 90 b = 212.561 β = 96.72 c = 55.752 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 PIXEL DECTRIS PILATUS3 6M 2015-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.166 106.28 96.1 0.108 0.994 8.4 3.3 54438 39.65
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.166 2.173 99.5 0.642 0.708 2.1 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2shp 2.166 106.28 54385 2680 96 0.1943 0.1922 0.2356 0.2574 RANDOM 36.33
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] -3.2974 0.7323 0.3963 2.9011
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.45 t_omega_torsion 3.17 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.45 t_omega_torsion 3.17 t_angle_deg 0.96 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7813 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 86
Software Software Software Name Purpose BUSTER refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction BUSTER phasing