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Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with S-naringenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Protein incubated with 1mM UDP- 5 mM naringenin, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5,
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.42 49.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.728 α = 90 b = 167.566 β = 90 c = 63.108 γ = 90
Symmetry Space Group P 21 21 2
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 2022-03-13 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 2.7 40 99.9 0.149 0.055 0.996 17.2 7.3 26941 -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 2.7 2.75 100 1.133 0.43 0.73 1.9 6.8
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 2.7 35.751 26847 1289 99.699 0.181 0.1781 0.1831 0.2416 0.2392 56.351
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] -1.177 0.041 1.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.318 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_2_deg 11.956 r_lrange_other 9.21 r_lrange_it 9.208 r_dihedral_angle_1_deg 6.367 r_scangle_it 5.766 r_scangle_other 5.766 r_mcangle_it 4.441 r_mcangle_other 4.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.318 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_2_deg 11.956 r_lrange_other 9.21 r_lrange_it 9.208 r_dihedral_angle_1_deg 6.367 r_scangle_it 5.766 r_scangle_other 5.766 r_mcangle_it 4.441 r_mcangle_other 4.441 r_scbond_it 3.516 r_scbond_other 3.515 r_mcbond_it 2.743 r_mcbond_other 2.737 r_angle_refined_deg 1.351 r_angle_other_deg 0.719 r_nbd_other 0.225 r_nbd_refined 0.221 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.125 r_ncsr_local_group_1 0.094 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_refined 0.067 r_chiral_restr 0.062 r_symmetry_xyhbond_nbd_other 0.014 r_bond_refined_d 0.008 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6623 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement SERGUI data collection HKL-3000 data reduction MOLREP phasing HKL-3000 data scaling