☰ Navigation Tabs
Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with kaempferol
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 7.5 293 Protein incubated with 1 mM UDP and kaempferol dissolved in ethanol.
0.2 M Ammonium sulfate
0.1 M HEPES pH 7.5
25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.78 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.277 α = 90 b = 159.906 β = 90 c = 163.311 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 2022-03-13 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 2.75 40 95.7 0.183 0.072 0.985 14 6.2 56602 -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 2.82 98.4 0.846 0.313 0.829 2.1 6.6
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 39.588 54951 2773 95.592 0.193 0.1915 0.1919 0.2316 0.228 71.855
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] 1.468 -0.83 -0.638
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.075 r_dihedral_angle_3_deg 15.562 r_lrange_other 13.134 r_lrange_it 13.131 r_scangle_it 8.724 r_scangle_other 8.724 r_mcangle_it 7.718 r_mcangle_other 7.718 r_dihedral_angle_1_deg 6.711 r_scbond_it 5.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.075 r_dihedral_angle_3_deg 15.562 r_lrange_other 13.134 r_lrange_it 13.131 r_scangle_it 8.724 r_scangle_other 8.724 r_mcangle_it 7.718 r_mcangle_other 7.718 r_dihedral_angle_1_deg 6.711 r_scbond_it 5.785 r_scbond_other 5.785 r_mcbond_it 5.226 r_mcbond_other 5.226 r_dihedral_angle_2_deg 3.262 r_angle_refined_deg 1.518 r_angle_other_deg 0.823 r_symmetry_nbd_other 0.217 r_nbd_other 0.21 r_nbd_refined 0.203 r_symmetry_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.137 r_ncsr_local_group_1 0.093 r_ncsr_local_group_5 0.092 r_ncsr_local_group_3 0.091 r_ncsr_local_group_2 0.089 r_ncsr_local_group_4 0.089 r_ncsr_local_group_6 0.082 r_symmetry_nbtor_other 0.07 r_chiral_restr 0.063 r_bond_refined_d 0.015 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 13198 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 186
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing SERGUI data collection