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Glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Complex with UDP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.9 289 To produce cocrystals of the UDP complex His6-tagged apo-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9, 150 mM NaCl was incubated with UDP at a final concentration of 1 mM. Crystals formed in 0.1 M Bis-Tris pH 7.5, 0.2 M potassium thiocyanate, 20 % (w/v) PEG 3350 after 14 days
Crystal Properties Matthews coefficient Solvent content 2.23 44.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.406 α = 90 b = 70.687 β = 91.374 c = 140.312 γ = 90
Symmetry Space Group P 1 21 1
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 PILATUS3 6M 2021-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9795 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 70.234 99.55 0.2 0.982 5.15 7 43913 49.36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 0.88
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 2.6 70.234 43889 2166 99.939 0.228 0.2257 0.2252 0.2761 0.278 70.527
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] 3.169 0.631 -0.556 -2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.176 r_dihedral_angle_6_deg 14.254 r_dihedral_angle_2_deg 7.836 r_dihedral_angle_1_deg 7.82 r_lrange_it 5.972 r_lrange_other 5.972 r_scangle_it 3.597 r_scangle_other 3.597 r_mcangle_it 2.988 r_mcangle_other 2.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.176 r_dihedral_angle_6_deg 14.254 r_dihedral_angle_2_deg 7.836 r_dihedral_angle_1_deg 7.82 r_lrange_it 5.972 r_lrange_other 5.972 r_scangle_it 3.597 r_scangle_other 3.597 r_mcangle_it 2.988 r_mcangle_other 2.988 r_scbond_it 2.216 r_scbond_other 2.216 r_angle_refined_deg 1.826 r_mcbond_it 1.81 r_mcbond_other 1.809 r_angle_other_deg 0.637 r_symmetry_nbd_refined 0.367 r_nbd_other 0.292 r_nbd_refined 0.229 r_symmetry_nbd_other 0.205 r_xyhbond_nbd_refined 0.204 r_nbtor_refined 0.191 r_symmetry_xyhbond_nbd_other 0.181 r_ncsr_local_group_3 0.148 r_ncsr_local_group_6 0.148 r_ncsr_local_group_5 0.145 r_symmetry_xyhbond_nbd_refined 0.125 r_ncsr_local_group_1 0.125 r_ncsr_local_group_4 0.122 r_ncsr_local_group_2 0.106 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10569 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing