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Crystal structure of human tyrosylprotein sulfotransferase 2 (TPST2) in cation-bound state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 0.1M HEPES-NaOH (pH 7.0), 16% (w/v) PEG 6000, 0.1M Potassium sodium tartrate, 20mM ZnCl2
Crystal Properties Matthews coefficient Solvent content 3.77 67.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.254 α = 90 b = 102.254 β = 90 c = 103.6 γ = 90
Symmetry Space Group P 43 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER2 X 9M 2025-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0000 PAL/PLS 5C (4A)
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 1.75 46.21 100 0.144 0.999 18.7 26.8 55466
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 1.75 1.79 99.2 1.235 0.76 3.5 26.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.75 46.21 1.34 55401 2005 99.91 0.1715 0.1709 0.1698 0.1876 0.1852 24.29
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 12.8405 f_angle_d 0.9001 f_chiral_restr 0.0549 f_plane_restr 0.008 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2339 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 47
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX phasing PHENIX refinement Coot model building