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Characterization and engineering of the bifunctional N- and O- glucosyltransferase involved in xenobiotic metabolism in plants
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VCH PDB ENTRY 2VCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 29% (W/V) PEG 3350, 0.1M TRIS PH 8.0
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.642 α = 90 b = 94.418 β = 110.35 c = 56.676 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2006-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 30 97.7 0.09 14.7 3.6 47687
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 100 0.45 4.25 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VCH 1.75 52.49 44219 2361 97.7 0.173 0.171 0.1706 0.209 0.2091 RANDOM 16.25
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] -0.28 -0.16 0.62 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_4_deg 17.1 r_dihedral_angle_3_deg 13.02 r_dihedral_angle_1_deg 5.93 r_scangle_it 3.536 r_scbond_it 2.431 r_angle_refined_deg 1.615 r_mcangle_it 1.565 r_mcbond_it 1.042 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.15 r_dihedral_angle_4_deg 17.1 r_dihedral_angle_3_deg 13.02 r_dihedral_angle_1_deg 5.93 r_scangle_it 3.536 r_scbond_it 2.431 r_angle_refined_deg 1.615 r_mcangle_it 1.565 r_mcbond_it 1.042 r_nbtor_refined 0.31 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 3599 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling