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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 switch 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 7.1 293 31.7% (w/v) PEG 3350, 0.1 M HEPES, 0.233 M MgSO4
Crystal Properties Matthews coefficient Solvent content 1.85 34.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.035 α = 90 b = 30.035 β = 90 c = 213.113 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 2.89 53.28 100 0.182 0.074 0.998 10.4 13.8 4283 -3 61.79
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 2.89 3.07 100 1.316 0.552 0.764 2 13.2
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 2.89 53.28 3811 418 99.98 0.24372 0.23943 0.2404 0.28462 0.2942 RANDOM 70.991
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] -0.32 -0.32 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.873 r_dihedral_angle_4_deg 23.298 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_1_deg 6.127 r_angle_refined_deg 1.252 r_long_range_B_refined 1.041 r_long_range_B_other 1.041 r_angle_other_deg 0.978 r_mcangle_it 0.236 r_mcangle_other 0.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.873 r_dihedral_angle_4_deg 23.298 r_dihedral_angle_3_deg 16.305 r_dihedral_angle_1_deg 6.127 r_angle_refined_deg 1.252 r_long_range_B_refined 1.041 r_long_range_B_other 1.041 r_angle_other_deg 0.978 r_mcangle_it 0.236 r_mcangle_other 0.236 r_scangle_other 0.13 r_mcbond_other 0.126 r_mcbond_it 0.125 r_chiral_restr 0.073 r_scbond_it 0.063 r_scbond_other 0.063 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 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 1808 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing