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Glycosyltransferase C from the Limosilactobacillus reuteri accessory secretion system. Complex with UDP-GlcNAc.
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 7.1 289 ammonium hydrogen citrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.639 α = 90 b = 121.392 β = 90 c = 174.099 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) 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 2.4 60.7 99.68 0.099 0.99 5.62 6.6 64276 46.52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.9018 0.516 0.58
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 2.4 60.7 64220 3212 99.904 0.191 0.1892 0.1829 0.2312 0.2288 48.405
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] -0.744 1.358 -0.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.569 r_dihedral_angle_6_deg 15.126 r_dihedral_angle_2_deg 10.136 r_lrange_it 8.701 r_lrange_other 8.7 r_scangle_it 7.436 r_scangle_other 7.436 r_dihedral_angle_1_deg 6.835 r_scbond_it 5.086 r_scbond_other 5.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.569 r_dihedral_angle_6_deg 15.126 r_dihedral_angle_2_deg 10.136 r_lrange_it 8.701 r_lrange_other 8.7 r_scangle_it 7.436 r_scangle_other 7.436 r_dihedral_angle_1_deg 6.835 r_scbond_it 5.086 r_scbond_other 5.07 r_dihedral_angle_other_2_deg 4.699 r_mcangle_it 4.138 r_mcangle_other 4.138 r_mcbond_it 2.683 r_mcbond_other 2.681 r_angle_refined_deg 2.469 r_angle_other_deg 0.833 r_nbd_other 0.234 r_nbd_refined 0.229 r_symmetry_nbd_refined 0.226 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.2 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.122 r_ncsr_local_group_3 0.116 r_ncsr_local_group_5 0.116 r_ncsr_local_group_1 0.115 r_ncsr_local_group_6 0.111 r_ncsr_local_group_2 0.108 r_ncsr_local_group_4 0.101 r_symmetry_nbtor_other 0.094 r_symmetry_xyhbond_nbd_other 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10844 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHENIX phasing