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Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based inhibitory motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 291 31.7% (w/v) PEG3350, 0.1 M HEPES, 0.233 M MgSO4
Crystal Properties Matthews coefficient Solvent content 1.82 32.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.856 α = 90 b = 29.856 β = 90 c = 208.227 γ = 90
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 PILATUS 2M-F Toroidal focusing mirrors 2016-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00002 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.095 52.06 100 0.053 0.079 0.946 11.2 13.8 10722 -3 18.758
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.095 2.16 100 1.149 0.484 0.526 2 12.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3TKZ 2.1 52.06 10137 513 99.99 0.22794 0.22525 0.2302 0.2785 0.2798 RANDOM 35.16
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] -0.23 -0.23 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.829 r_dihedral_angle_4_deg 20.755 r_dihedral_angle_3_deg 14.862 r_long_range_B_other 9.252 r_long_range_B_refined 9.237 r_scangle_other 8.657 r_dihedral_angle_1_deg 6.472 r_scbond_it 6.424 r_scbond_other 6.403 r_mcangle_it 5.646
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.829 r_dihedral_angle_4_deg 20.755 r_dihedral_angle_3_deg 14.862 r_long_range_B_other 9.252 r_long_range_B_refined 9.237 r_scangle_other 8.657 r_dihedral_angle_1_deg 6.472 r_scbond_it 6.424 r_scbond_other 6.403 r_mcangle_it 5.646 r_mcangle_other 5.645 r_mcbond_it 3.806 r_mcbond_other 3.792 r_angle_refined_deg 1.376 r_angle_other_deg 0.916 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1796 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing