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Crystal structure of a sulfotransferase S4 in complex with PAP and PNPS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 1.6 M (NH4)2SO4, 0.1 M MES pH 6.0, 1% dextran sulfate sodium salt 8000
Crystal Properties Matthews coefficient Solvent content 3.07 59.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.045 α = 90 b = 78.045 β = 90 c = 140.124 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 6M 2023-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17UM 0.9785 SSRF BL17UM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.78 43.35 100 0.073 0.075 0.014 1 33 27.7 42303
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.82 99.3 0.97 1.001 0.241 0.878 16.2
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 1.78 43.35 1.35 42216 2112 99.93 0.1791 0.1777 0.1825 0.2043 0.2075
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 7.405 f_angle_d 1.157 f_chiral_restr 0.078 f_bond_d 0.013 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2442 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing