6JEN

Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro-glucose and pterostilbene


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.11 M potassium citrate 0.06 M lithium citrate 0.11 M sodium phosphate 23-25% w/v PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.4750.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.718α = 90
b = 136.883β = 90
c = 205.136γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2018-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.655099.80.0710.07715.76.647340
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.7498.60.6942

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2VCH2.6549.6844937232899.70.196990.194440.24763RANDOM85
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.922
r_dihedral_angle_4_deg18.389
r_dihedral_angle_3_deg17.964
r_long_range_B_refined17.401
r_long_range_B_other17.401
r_scangle_other12.435
r_mcangle_it11.992
r_mcangle_other11.992
r_scbond_it8.609
r_scbond_other8.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.922
r_dihedral_angle_4_deg18.389
r_dihedral_angle_3_deg17.964
r_long_range_B_refined17.401
r_long_range_B_other17.401
r_scangle_other12.435
r_mcangle_it11.992
r_mcangle_other11.992
r_scbond_it8.609
r_scbond_other8.609
r_mcbond_it8.456
r_mcbond_other8.453
r_dihedral_angle_1_deg7.184
r_angle_other_deg2.316
r_angle_refined_deg1.551
r_chiral_restr0.073
r_bond_other_d0.035
r_bond_refined_d0.009
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10087
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms165

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing