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Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VB158
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G0M
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 2.5 50.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.829 α = 90 b = 44.476 β = 97.629 c = 137.577 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 XE 16M 2021-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97624 Diamond I03
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 1.55 39.21 96.8 0.966 2.9 5.8 70791
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 1.55 1.58 0.616
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 5g0m 1.55 39.21 70705 3509 96.362 0.221 0.2198 0.2254 0.2519 0.2552 19.243
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] -1.158 0.444 1.952 -0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.268 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_4_deg 13.063 r_dihedral_angle_1_deg 6.594 r_lrange_it 4.759 r_lrange_other 4.669 r_scangle_other 3.036 r_scangle_it 3.035 r_mcangle_it 2.331 r_mcangle_other 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.268 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_4_deg 13.063 r_dihedral_angle_1_deg 6.594 r_lrange_it 4.759 r_lrange_other 4.669 r_scangle_other 3.036 r_scangle_it 3.035 r_mcangle_it 2.331 r_mcangle_other 2.33 r_scbond_it 1.983 r_scbond_other 1.979 r_angle_refined_deg 1.584 r_mcbond_it 1.491 r_mcbond_other 1.491 r_angle_other_deg 1.399 r_nbd_refined 0.202 r_symmetry_nbd_other 0.175 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.165 r_nbd_other 0.165 r_symmetry_xyhbond_nbd_refined 0.164 r_symmetry_nbd_refined 0.153 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.075 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 3341 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing