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Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with covalent inhibitor ME727
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 49.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.656 α = 90 b = 44.469 β = 97.61 c = 136.714 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 PILATUS 6M-F 2019-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.911880 Diamond I04-1
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 1.25 74.62 98.4 0.993 6.6 3.7 133814
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 1.25 1.27 0.68
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 1.25 74.6 133776 6617 98.07 0.169 0.1685 0.178 0.1841 0.1904 13.788
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] -0.585 0.52 0.449 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.432 r_dihedral_angle_4_deg 15.297 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_1_deg 6.262 r_lrange_it 4.527 r_lrange_other 4.302 r_scangle_it 3.34 r_scangle_other 3.329 r_angle_other_deg 2.388 r_scbond_it 2.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.432 r_dihedral_angle_4_deg 15.297 r_dihedral_angle_3_deg 12.201 r_dihedral_angle_1_deg 6.262 r_lrange_it 4.527 r_lrange_other 4.302 r_scangle_it 3.34 r_scangle_other 3.329 r_angle_other_deg 2.388 r_scbond_it 2.298 r_scbond_other 2.203 r_mcangle_it 1.942 r_mcangle_other 1.942 r_angle_refined_deg 1.803 r_mcbond_it 1.301 r_mcbond_other 1.28 r_nbd_refined 0.212 r_symmetry_nbd_other 0.21 r_symmetry_xyhbond_nbd_refined 0.2 r_nbd_other 0.197 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.111 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.081 r_bond_other_d 0.036 r_gen_planes_other 0.02 r_bond_refined_d 0.016 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3458 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing