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Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with quercetin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8GKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Quercetin dissolved in ETOH and let it evaporate on plate.
Protein incubated with UDP.
0.2 M Ammonium acetate
0.1 M BIS-TRIS pH 6.5
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.13 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.884 α = 90 b = 109.42 β = 90 c = 165.84 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2022-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.75 40 92 0.209 0.086 0.96 11.8 5.7 10446 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 79.9 0.629 0.258 0.886 1.9 5.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.75 38.916 10391 491 92.111 0.21 0.2073 0.1971 0.2641 0.2654 69.584
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] 1.171 -0.694 -0.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.489 r_dihedral_angle_3_deg 14.028 r_lrange_it 12.693 r_lrange_other 12.691 r_scangle_it 9.945 r_scangle_other 9.917 r_mcangle_it 7.102 r_mcangle_other 7.1 r_dihedral_angle_2_deg 6.815 r_scbond_it 6.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.489 r_dihedral_angle_3_deg 14.028 r_lrange_it 12.693 r_lrange_other 12.691 r_scangle_it 9.945 r_scangle_other 9.917 r_mcangle_it 7.102 r_mcangle_other 7.1 r_dihedral_angle_2_deg 6.815 r_scbond_it 6.626 r_scbond_other 6.624 r_dihedral_angle_1_deg 6.135 r_mcbond_it 4.655 r_mcbond_other 4.654 r_angle_refined_deg 1.474 r_angle_other_deg 1.004 r_nbd_other 0.233 r_nbd_refined 0.221 r_symmetry_nbd_other 0.22 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.141 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_refined 0.079 r_symmetry_xyhbond_nbd_other 0.037 r_bond_refined_d 0.007 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3187 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing SERGUI data collection