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Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with UDP-glucose
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 7 293 5% Tacsimate pH 7, 0.1 M HEPES pH 7, 10% PEG 5000. Protein soaked in UDP-glucose
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.231 α = 90 b = 77.231 β = 90 c = 164.197 γ = 90
Symmetry Space Group P 41 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 2021-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.000 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim 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 2.35 40 95.9 0.113 0.046 18.6 5.3 20661 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 97.9 0.749 0.319 2.4 5
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 2.35 38.688 20544 1047 95.651 0.22 0.2178 0.2204 0.2688 0.2683 37.852
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] -0.703 -0.703 1.405
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.464 r_dihedral_angle_4_deg 23.736 r_dihedral_angle_3_deg 14.753 r_dihedral_angle_1_deg 6.996 r_lrange_it 4.357 r_lrange_other 4.337 r_scangle_it 2.567 r_scangle_other 2.566 r_mcangle_it 2.236 r_mcangle_other 2.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.464 r_dihedral_angle_4_deg 23.736 r_dihedral_angle_3_deg 14.753 r_dihedral_angle_1_deg 6.996 r_lrange_it 4.357 r_lrange_other 4.337 r_scangle_it 2.567 r_scangle_other 2.566 r_mcangle_it 2.236 r_mcangle_other 2.236 r_scbond_it 1.519 r_scbond_other 1.518 r_angle_refined_deg 1.453 r_mcbond_it 1.334 r_mcbond_other 1.331 r_angle_other_deg 1.261 r_symmetry_nbd_refined 0.253 r_nbd_other 0.234 r_nbd_refined 0.201 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing SERGUI data collection