2VCH

Characterization and engineering of the bifunctional N- and O- glucosyltransferase involved in xenobiotic metabolism in plants


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ACVPDB ENTRY 1ACV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
123 % (W/V) PEG 3350, 0.1 M MMT (MALIC ACID, MES, TRIS BUFFER) PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.68α = 90
b = 94.006β = 110.24
c = 56.992γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCD2006-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.4553.4599.90.0516.94.2832742
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.5399.40.225.53.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1ACV1.4553.4578900415399.80.1790.1780.196RANDOM14.12
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]
-0.23-0.020.72-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.076
r_dihedral_angle_4_deg15.312
r_dihedral_angle_3_deg12.749
r_dihedral_angle_1_deg5.712
r_scangle_it3.627
r_scbond_it2.413
r_mcangle_it1.694
r_angle_refined_deg1.627
r_mcbond_it1.111
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.076
r_dihedral_angle_4_deg15.312
r_dihedral_angle_3_deg12.749
r_dihedral_angle_1_deg5.712
r_scangle_it3.627
r_scbond_it2.413
r_mcangle_it1.694
r_angle_refined_deg1.627
r_mcbond_it1.111
r_nbtor_refined0.312
r_symmetry_vdw_refined0.239
r_nbd_refined0.215
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.137
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3570
Nucleic Acid Atoms
Solvent Atoms444
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing