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Glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Apo form.
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 apo-enzyme crystallisation screening were conducted with the purified His6-tag-LrGtfC100-23 at a concentration of 10 mg/mL in 20 mM Tris pH 7.9 200 mM NaCl. Crystals formed in 0.1 M Bis-Tris pH 7.5, 0.2 M potassium thiocyanate, 20% (w/v) polyethylene glycol (PEG) 3350 after 14-days.
Crystal Properties Matthews coefficient Solvent content 2.23 44.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.439 α = 90 b = 140.491 β = 90 c = 145.324 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 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 72.768 99.63 0.112 0.997 20.47 20 98062 40.62
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 2.07 0.781
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 72.768 98015 5101 99.922 0.21 0.2072 0.2018 0.2528 0.2484 70.448
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] -0.597 -3.023 3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.92 r_dihedral_angle_6_deg 14.987 r_dihedral_angle_2_deg 13.32 r_lrange_other 10.382 r_lrange_it 10.376 r_scangle_it 7.939 r_scangle_other 7.938 r_dihedral_angle_1_deg 7.511 r_mcangle_it 6.276 r_mcangle_other 6.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.92 r_dihedral_angle_6_deg 14.987 r_dihedral_angle_2_deg 13.32 r_lrange_other 10.382 r_lrange_it 10.376 r_scangle_it 7.939 r_scangle_other 7.938 r_dihedral_angle_1_deg 7.511 r_mcangle_it 6.276 r_mcangle_other 6.275 r_scbond_it 5.725 r_scbond_other 5.725 r_mcbond_it 4.632 r_mcbond_other 4.632 r_angle_refined_deg 2.248 r_angle_other_deg 0.913 r_symmetry_nbd_refined 0.28 r_symmetry_xyhbond_nbd_refined 0.254 r_nbd_other 0.214 r_nbd_refined 0.206 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.171 r_symmetry_nbd_other 0.168 r_ncsr_local_group_6 0.14 r_ncsr_local_group_2 0.135 r_ncsr_local_group_3 0.132 r_chiral_restr 0.131 r_ncsr_local_group_4 0.127 r_ncsr_local_group_1 0.122 r_ncsr_local_group_5 0.122 r_symmetry_nbtor_other 0.078 r_xyhbond_nbd_other 0.02 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10810 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing