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The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophotetraose observed as sophorose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VKW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.135 α = 90 b = 71.615 β = 104.894 c = 130.308 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 210 2017-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.79 47.93 100 0.995 9.4 3.8 138455
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 1.79 1.82 99.7 0.57 1.6 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 7VKW 1.79 47.905 138450 6808 99.969 0.168 0.1663 0.1775 0.2005 0.2071 17.597
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] 0.01 0.02 -0.011 -0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.082 r_dihedral_angle_4_deg 20.766 r_dihedral_angle_3_deg 14.266 r_dihedral_angle_1_deg 7.004 r_lrange_it 4.822 r_lrange_other 4.822 r_scangle_it 3.625 r_scangle_other 3.625 r_scbond_it 2.283 r_scbond_other 2.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.082 r_dihedral_angle_4_deg 20.766 r_dihedral_angle_3_deg 14.266 r_dihedral_angle_1_deg 7.004 r_lrange_it 4.822 r_lrange_other 4.822 r_scangle_it 3.625 r_scangle_other 3.625 r_scbond_it 2.283 r_scbond_other 2.283 r_mcangle_it 2.255 r_mcangle_other 2.255 r_angle_refined_deg 1.591 r_mcbond_it 1.518 r_mcbond_other 1.505 r_angle_other_deg 1.381 r_symmetry_nbd_refined 0.35 r_nbd_other 0.3 r_nbd_refined 0.208 r_nbtor_refined 0.177 r_symmetry_nbd_other 0.176 r_xyhbond_nbd_refined 0.15 r_metal_ion_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.119 r_symmetry_metal_ion_refined 0.087 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.049 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11687 Nucleic Acid Atoms Solvent Atoms 863 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing