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Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with naringin
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 Protein incubated with 1mM UDP and 2.5 mM naringin
0.2 M Sodium Chloride
0.1 M BIS-TRIS pH 6.5
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.33 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.482 α = 90 b = 115.677 β = 90 c = 165.693 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 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 1.8 40 97.4 0.093 0.035 0.992 27.7 6.7 83547 -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 1.8 1.83 96.4 0.843 0.301 0.894 1.9 6.9
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 1.8 34.402 83401 4170 97.403 0.182 0.18 0.1902 0.2138 0.2227 33.838
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] -0.042 1.448 -1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.675 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_2_deg 9.95 r_lrange_it 6.124 r_dihedral_angle_1_deg 6.09 r_lrange_other 6.061 r_scangle_it 4.007 r_scangle_other 4.007 r_mcangle_other 2.631 r_mcangle_it 2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.675 r_dihedral_angle_3_deg 14.161 r_dihedral_angle_2_deg 9.95 r_lrange_it 6.124 r_dihedral_angle_1_deg 6.09 r_lrange_other 6.061 r_scangle_it 4.007 r_scangle_other 4.007 r_mcangle_other 2.631 r_mcangle_it 2.63 r_scbond_it 2.587 r_scbond_other 2.586 r_mcbond_it 1.786 r_mcbond_other 1.786 r_angle_refined_deg 1.671 r_angle_other_deg 0.864 r_symmetry_nbd_refined 0.271 r_nbd_other 0.27 r_nbd_refined 0.215 r_symmetry_nbd_other 0.213 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.151 r_ncsr_local_group_1 0.095 r_symmetry_xyhbond_nbd_refined 0.093 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.017 r_gen_planes_other 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6549 Nucleic Acid Atoms Solvent Atoms 609 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing SERGUI data collection