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The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophorose
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) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.53 α = 90 b = 71.66 β = 106.02 c = 129.82 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 2017-02-22 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) R Merge I (Observed) 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 57.14 99.9 0.1 9.4 3.2 307557
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 99.9 0.386 3.3
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 55.312 97540 4785 99.82 0.168 0.1656 0.175 0.204 0.2103 15.008
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] -0.003 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_4_deg 21.438 r_dihedral_angle_3_deg 14.829 r_dihedral_angle_1_deg 7.184 r_lrange_it 4.159 r_lrange_other 4.159 r_scangle_it 2.994 r_scangle_other 2.993 r_mcangle_it 2.029 r_mcangle_other 2.029
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.445 r_dihedral_angle_4_deg 21.438 r_dihedral_angle_3_deg 14.829 r_dihedral_angle_1_deg 7.184 r_lrange_it 4.159 r_lrange_other 4.159 r_scangle_it 2.994 r_scangle_other 2.993 r_mcangle_it 2.029 r_mcangle_other 2.029 r_scbond_it 1.841 r_scbond_other 1.841 r_angle_refined_deg 1.577 r_angle_other_deg 1.334 r_mcbond_it 1.276 r_mcbond_other 1.276 r_nbd_refined 0.202 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.177 r_nbd_other 0.177 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_metal_ion_refined 0.119 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.077 r_metal_ion_refined 0.061 r_bond_refined_d 0.01 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 11633 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing