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The complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with p-nitrophenyl-alpha-D-glucopyranoside
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 = 163.576 α = 90 b = 71.533 β = 105.794 c = 129.872 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 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 1.79 47.86 99.9 0.084 8.4 3.8 135895
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 1.79 1.82 99.8 0.541 1.7 3.6
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 1.79 19.891 135778 6826 99.846 0.182 0.1798 0.189 0.2183 0.2265 20.756
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 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.973 r_dihedral_angle_4_deg 20.145 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_1_deg 6.954 r_lrange_it 4.613 r_lrange_other 4.566 r_scangle_it 3.623 r_scangle_other 3.623 r_scbond_it 2.322 r_scbond_other 2.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.973 r_dihedral_angle_4_deg 20.145 r_dihedral_angle_3_deg 14.974 r_dihedral_angle_1_deg 6.954 r_lrange_it 4.613 r_lrange_other 4.566 r_scangle_it 3.623 r_scangle_other 3.623 r_scbond_it 2.322 r_scbond_other 2.322 r_mcangle_it 2.277 r_mcangle_other 2.276 r_mcbond_it 1.581 r_mcbond_other 1.58 r_angle_refined_deg 1.557 r_angle_other_deg 1.357 r_nbd_other 0.226 r_nbd_refined 0.204 r_symmetry_nbd_refined 0.19 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.183 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.143 r_symmetry_metal_ion_refined 0.097 r_metal_ion_refined 0.095 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.052 r_bond_refined_d 0.009 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 11651 Nucleic Acid Atoms Solvent Atoms 815 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing