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Crystal structure of PTPN2 catalytic domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1L8K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 0.1 M Bis-Tris Propane (pH-7.5), 0.2 M Sodium Iodide, 20% w/v PEG 3350, 10% v/v Ethylene glycol and 0.9 mM Mitoxantrone additive
Crystal Properties Matthews coefficient Solvent content 2.31 46.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.094 α = 111.54 b = 68.187 β = 102.659 c = 72.683 γ = 92.337
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 107 CCD RAYONIX MX300HE 2019-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
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 1.7 25 96.4 0.022 0.98 33.7 2.5 100918
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 1.7 1.76 95.5 0.238 0.92 4.1 2.5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1L8K 1.7 24.848 100506 4866 95.952 0.201 0.1989 0.241 0.2557 19.305
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] -0.062 0.131 0.056 -0.04 0.022 0.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.269 r_dihedral_angle_4_deg 20.315 r_dihedral_angle_3_deg 16.42 r_dihedral_angle_1_deg 6.752 r_lrange_it 5.512 r_lrange_other 5.421 r_scangle_it 3.824 r_scangle_other 3.819 r_mcangle_it 2.771 r_mcangle_other 2.771
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.269 r_dihedral_angle_4_deg 20.315 r_dihedral_angle_3_deg 16.42 r_dihedral_angle_1_deg 6.752 r_lrange_it 5.512 r_lrange_other 5.421 r_scangle_it 3.824 r_scangle_other 3.819 r_mcangle_it 2.771 r_mcangle_other 2.771 r_scbond_it 2.416 r_scbond_other 2.41 r_mcbond_it 1.848 r_mcbond_other 1.845 r_angle_refined_deg 1.666 r_angle_other_deg 1.395 r_symmetry_xyhbond_nbd_other 0.379 r_symmetry_nbd_refined 0.247 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.211 r_nbd_other 0.192 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.17 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6955 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing