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Structure of Phytolacca americana UGT2 complexed with UDP-2fluoro-glucose and resveratrol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.11 M potassium citrate
0.06 M lithium citrate
0.11 M sodium phosphate
23% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.55 51.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.374 α = 90 b = 137.616 β = 90 c = 208.956 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2017-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.6 50 99 0.086 0.04 25.9 6.8 51665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.514 0.689 1.5 7.2
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 2VCH 2.6 44.85 48996 2598 98.84 0.19573 0.1927 0.1946 0.25225 0.2494 RANDOM 75.087
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.52 r_dihedral_angle_4_deg 20.347 r_dihedral_angle_3_deg 17.754 r_long_range_B_refined 14.481 r_long_range_B_other 14.481 r_scangle_other 11.43 r_mcangle_it 10.742 r_mcangle_other 10.742 r_scbond_it 7.908 r_scbond_other 7.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.52 r_dihedral_angle_4_deg 20.347 r_dihedral_angle_3_deg 17.754 r_long_range_B_refined 14.481 r_long_range_B_other 14.481 r_scangle_other 11.43 r_mcangle_it 10.742 r_mcangle_other 10.742 r_scbond_it 7.908 r_scbond_other 7.908 r_mcbond_it 7.68 r_mcbond_other 7.679 r_dihedral_angle_1_deg 7.117 r_angle_other_deg 2.32 r_angle_refined_deg 1.558 r_chiral_restr 0.075 r_bond_other_d 0.035 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 10087 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 159
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing