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Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with glucuronic acid configured 3-geminal diol iminosugar inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PSH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.5 M AmSO4 1 M LiSO4 0.1 M Trisodium Citrate
Crystal Properties Matthews coefficient Solvent content 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.037 α = 90 b = 42.614 β = 99.417 c = 140.141 γ = 90
Symmetry Space Group I 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 PIXEL DECTRIS EIGER2 X 16M 2021-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 Diamond I04
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 1.5 40.756 100 0.999 11 6.4 76979
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 1.5 1.53 0.545
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 1.5 40.756 76978 3861 99.949 0.2 0.1989 0.2068 0.2231 0.2288 22.124
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] -0.264 0.532 0.871 -0.743
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.899 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 14.187 r_dihedral_angle_1_deg 6.846 r_lrange_other 5.825 r_lrange_it 5.824 r_scangle_it 4.881 r_scangle_other 4.881 r_scbond_it 3.269 r_scbond_other 3.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.899 r_dihedral_angle_4_deg 20.262 r_dihedral_angle_3_deg 14.187 r_dihedral_angle_1_deg 6.846 r_lrange_other 5.825 r_lrange_it 5.824 r_scangle_it 4.881 r_scangle_other 4.881 r_scbond_it 3.269 r_scbond_other 3.269 r_mcangle_it 2.867 r_mcangle_other 2.867 r_mcbond_it 2.037 r_mcbond_other 2.032 r_angle_refined_deg 1.771 r_angle_other_deg 1.524 r_nbd_other 0.222 r_nbd_refined 0.212 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.14 r_symmetry_nbd_refined 0.109 r_xyhbond_nbd_refined 0.099 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_chiral_restr_other 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 3417 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing