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Crystal structure of the C-terminal Fg domain of TNR with the single FN domain of PTPRZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J3F PDB entries 2J3F & 1FNA experimental model PDB 1FNA PDB entries 2J3F & 1FNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% w/v PEG2000 MME, 200 mM potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.325 α = 104.41 b = 75.656 β = 92.401 c = 88.322 γ = 91.811
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 2020-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.8 50 91.6 0.157 0.062 0.997 11.7 6.6 102222 25.57
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 1.8 1.86 91.1 0.991 0.517 0.486 1.1 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entries 2J3F & 1FNA 1.8 42.96 1.96 102103 2178 91.26 0.1747 0.174 0.2102 0.226 35.38
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.6919 f_angle_d 0.8767 f_chiral_restr 0.0627 f_bond_d 0.0107 f_plane_restr 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10361 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing