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The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with 1-Deoxynojirimycin
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 2.14 42.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.658 α = 90 b = 71.646 β = 106.338 c = 129.52 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 2017-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 47.58 100 0.105 15 7.6 96821
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 2.03 100 0.498 4.1 7.6
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 43.106 96817 4944 99.987 0.173 0.1713 0.1804 0.2076 0.2152 23.007
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] -0.002 -0.001 -0.001 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.855 r_dihedral_angle_4_deg 20.68 r_dihedral_angle_3_deg 14.897 r_dihedral_angle_1_deg 7.314 r_lrange_it 4.905 r_lrange_other 4.905 r_scangle_it 3.923 r_scangle_other 3.923 r_scbond_it 2.505 r_scbond_other 2.504
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.855 r_dihedral_angle_4_deg 20.68 r_dihedral_angle_3_deg 14.897 r_dihedral_angle_1_deg 7.314 r_lrange_it 4.905 r_lrange_other 4.905 r_scangle_it 3.923 r_scangle_other 3.923 r_scbond_it 2.505 r_scbond_other 2.504 r_mcangle_it 2.476 r_mcangle_other 2.476 r_mcbond_it 1.731 r_mcbond_other 1.73 r_angle_refined_deg 1.555 r_angle_other_deg 1.33 r_nbd_refined 0.202 r_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.185 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.168 r_xyhbond_nbd_refined 0.135 r_symmetry_metal_ion_refined 0.111 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.077 r_metal_ion_refined 0.058 r_chiral_restr_other 0.033 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 11626 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing