6LZX

Structure of Phytolacca americana UGT3 with 15-crown-5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.2 M Sodium Bromide 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.346.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.173α = 90
b = 103.298β = 90
c = 110.383γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.148.7399.60.160.170.070.999.76.519856
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)RedundancyNumber Unique Reflections (All)
13.13.31990.720.780.290.86.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2PQ63.10148.7261980596799.4980.2060.20270.259865.001
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]
-1.7572.213-0.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.941
r_dihedral_angle_3_deg19.011
r_dihedral_angle_4_deg18.531
r_lrange_it13.341
r_lrange_other13.341
r_mcangle_other7.769
r_mcangle_it7.768
r_scangle_it7.482
r_scangle_other7.481
r_dihedral_angle_1_deg7.049
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.941
r_dihedral_angle_3_deg19.011
r_dihedral_angle_4_deg18.531
r_lrange_it13.341
r_lrange_other13.341
r_mcangle_other7.769
r_mcangle_it7.768
r_scangle_it7.482
r_scangle_other7.481
r_dihedral_angle_1_deg7.049
r_mcbond_it4.934
r_mcbond_other4.926
r_scbond_it4.576
r_scbond_other4.576
r_angle_other_deg2.291
r_angle_refined_deg1.518
r_metal_ion_refined0.437
r_symmetry_nbd_other0.222
r_nbd_refined0.21
r_nbd_other0.196
r_symmetry_nbd_refined0.172
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.164
r_symmetry_xyhbond_nbd_refined0.126
r_ncsr_local_group_10.114
r_chiral_restr0.072
r_symmetry_nbtor_other0.069
r_bond_other_d0.035
r_ext_dist_refined_d0.021
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7271
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BALBESphasing