2VCE

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 2VCHPDB ENTRY 2VCH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
125 % (W/V) PEG 3350, 0.1 M TRIS PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.4149

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.807α = 90
b = 94.335β = 110.31
c = 57.059γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC CCD2006-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.919.6799.50.0818.82.9372802
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)
11.91.9799.50.3742.8

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 2VCH1.919.67350361865990.160.1580.198RANDOM17.88
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]
-0.25-0.261.1-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.699
r_dihedral_angle_4_deg17.503
r_dihedral_angle_3_deg14.419
r_dihedral_angle_1_deg6.485
r_scangle_it3.705
r_scbond_it2.574
r_angle_refined_deg1.647
r_mcangle_it1.611
r_mcbond_it1.019
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.699
r_dihedral_angle_4_deg17.503
r_dihedral_angle_3_deg14.419
r_dihedral_angle_1_deg6.485
r_scangle_it3.705
r_scbond_it2.574
r_angle_refined_deg1.647
r_mcangle_it1.611
r_mcbond_it1.019
r_nbtor_refined0.311
r_nbd_refined0.209
r_symmetry_vdw_refined0.205
r_xyhbond_nbd_refined0.152
r_symmetry_hbond_refined0.132
r_chiral_restr0.111
r_bond_refined_d0.018
r_gen_planes_refined0.007
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 Atoms3571
Nucleic Acid Atoms
Solvent Atoms402
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing