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Crystal structure of Phytolacca americana UGT3 with capsaicin and UDP-2fluoroglucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.15-0.20 M potassium acetate
20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.276 α = 90 b = 103.022 β = 90 c = 109.648 γ = 90
Symmetry Space Group P 21 21 21
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 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.6 50 99.59 0.07 0.07 0.03 0.99 17.86 6.8 33493 55.92
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 2.6 2.69 99.36 0.59 0.64 0.24 0.98 3.12 7.1
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 6LZY 2.6 46.62 1.35 33443 1638 99.48 0.207 0.2045 0.208 0.2578 0.259 57.94
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 24.7874 f_angle_d 0.7159 f_chiral_restr 0.0466 f_plane_restr 0.0043 f_bond_d 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7249 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 113
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing