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Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VB151
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 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.461 α = 90 b = 43.605 β = 98.685 c = 136.202 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 2021-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 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 1.62 74.924 99.7 0.99 10.1 6 61021
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 1.62 1.65 0.516 1.1
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 1.62 74.924 61021 2969 99.577 0.199 0.1976 0.2029 0.2259 0.2321 36.771
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] -0.693 3.922 0.278 -0.748
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.093 r_dihedral_angle_4_deg 16.6 r_dihedral_angle_3_deg 14.833 r_dihedral_angle_1_deg 6.554 r_lrange_it 6.463 r_lrange_other 6.451 r_scangle_other 4.949 r_scangle_it 4.945 r_mcangle_other 3.935 r_mcangle_it 3.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.093 r_dihedral_angle_4_deg 16.6 r_dihedral_angle_3_deg 14.833 r_dihedral_angle_1_deg 6.554 r_lrange_it 6.463 r_lrange_other 6.451 r_scangle_other 4.949 r_scangle_it 4.945 r_mcangle_other 3.935 r_mcangle_it 3.934 r_scbond_other 3.405 r_scbond_it 3.403 r_mcbond_it 2.975 r_mcbond_other 2.971 r_angle_refined_deg 1.567 r_angle_other_deg 1.432 r_symmetry_xyhbond_nbd_refined 0.225 r_nbd_other 0.219 r_nbd_refined 0.202 r_symmetry_nbd_other 0.194 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.166 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.075 r_symmetry_xyhbond_nbd_other 0.042 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3292 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing