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Crystal structure of Arabidopsis thaliana sulfotransferase SOT18 complexed with glucoraphanin precursor involved in glucosinolate biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MEK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.8 PEG
Crystal Properties Matthews coefficient Solvent content 2.85 56.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.55 α = 90 b = 63.9 β = 103.56 c = 53.11 γ = 90
Symmetry Space Group C 1 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 PILATUS3 2M 2022-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0000 SPring-8 BL45XU
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 1.39 63.46 95.1 0.994 7.45 5.8 81183
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 1.39 1.47 0.831
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5MEK 1.39 40.47 1.35 81160 1999 95.09 0.1354 0.1348 0.1361 0.1596 0.1596
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 9.237 f_angle_d 1.741 f_chiral_restr 0.108 f_bond_d 0.022 f_plane_restr 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2671 Nucleic Acid Atoms Solvent Atoms 465 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing