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Crystal structure of the PTPN3 PDZ domain bound to the PBM TACE C-terminal peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HKS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 20% w/v PEG 3350, 0.2 M NaSCN at pH 7
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.878 α = 90 b = 76.878 β = 90 c = 46.253 γ = 120
Symmetry Space Group P 32 2 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 EIGER X 16M 2018-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.98 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 66.58 99.5 0.997 12.51 13.9 17566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.761 0.887
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.7 66.58 16687 903 99.56 0.1694 0.16756 0.1551 0.20258 0.1948 RANDOM 42.01
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] 15.09 15.09 -30.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.601 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 16.563 r_long_range_B_other 9.961 r_long_range_B_refined 9.957 r_dihedral_angle_1_deg 7.964 r_scangle_other 7.408 r_mcangle_it 5.562 r_mcangle_other 5.557 r_scbond_it 5.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.601 r_dihedral_angle_4_deg 17.199 r_dihedral_angle_3_deg 16.563 r_long_range_B_other 9.961 r_long_range_B_refined 9.957 r_dihedral_angle_1_deg 7.964 r_scangle_other 7.408 r_mcangle_it 5.562 r_mcangle_other 5.557 r_scbond_it 5.273 r_scbond_other 5.255 r_mcbond_it 4.007 r_mcbond_other 4.003 r_angle_refined_deg 2.648 r_angle_other_deg 1.157 r_chiral_restr 0.158 r_bond_refined_d 0.029 r_gen_planes_refined 0.017 r_gen_planes_other 0.002 r_bond_other_d 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 784 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing