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Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor VL166
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 2.45 49.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.393 α = 90 b = 44.117 β = 97.579 c = 136.708 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 2020-01-18 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 1.55 75.11 99.9 0.997 7.1 3.9 71878
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 0.793
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 75.112 71856 3593 99.796 0.196 0.1946 0.2007 0.2227 0.2274 21.816
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] -1.535 0.684 3.605 -2.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.61 r_dihedral_angle_4_deg 16.476 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 6.689 r_lrange_it 5.329 r_lrange_other 5.236 r_scangle_it 3.799 r_scangle_other 3.798 r_mcangle_other 2.576 r_mcangle_it 2.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.61 r_dihedral_angle_4_deg 16.476 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 6.689 r_lrange_it 5.329 r_lrange_other 5.236 r_scangle_it 3.799 r_scangle_other 3.798 r_mcangle_other 2.576 r_mcangle_it 2.574 r_angle_other_deg 2.527 r_scbond_it 2.497 r_scbond_other 2.497 r_mcbond_it 1.752 r_mcbond_other 1.729 r_angle_refined_deg 1.643 r_symmetry_nbd_other 0.213 r_symmetry_xyhbond_nbd_refined 0.209 r_nbd_refined 0.206 r_chiral_restr 0.2 r_nbd_other 0.198 r_symmetry_nbd_refined 0.191 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.15 r_symmetry_nbtor_other 0.08 r_bond_other_d 0.036 r_gen_planes_other 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_other 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3312 Nucleic Acid Atoms Solvent Atoms 360 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing