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Crystal structure of human tyrosylprotein sulfotransferase 2 (TPST2) in Mn2+-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 (pH7.0), 14.2% (w/v) PEG 6000, 0.1M Potassium sodium tartrate, 1mM ZnCl2, 20mM MnCl2
Crystal Properties Matthews coefficient Solvent content 3.79 67.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.817 α = 90 b = 102.817 β = 90 c = 103.115 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 PILATUS3 6M 2025-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.9794 PAL/PLS 11C
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 2 46.09 100 0.176 0.999 24.4 25 38050 14.73
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 2 2.05 99.3 0.84 0.873 10.8 25.1
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2 46.09 1.33 37847 1885 99.48 0.1853 0.1832 0.2255 0.2053 18.89
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 14.0582 f_angle_d 0.9016 f_chiral_restr 0.051 f_plane_restr 0.0088 f_bond_d 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2334 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction XDS data scaling PHENIX phasing PHENIX refinement Coot model building