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Crystal structure of Beta-glucuronidase from Acidobacterium capsulatum in complex with competitive inhibitor derrived from siastatin B
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 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.75 α = 90 b = 44.67 β = 97.461 c = 136.268 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 2019-12-19 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 1.05 67.65 96.5 0.999 15.1 6.3 221410
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 1.05 1.07 0.582 1.4
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 1.05 67.648 221409 11011 96.299 0.167 0.1669 0.1759 0.1774 0.1846 13.041
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] -0.273 0.227 0.505 -0.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.268 r_dihedral_angle_4_deg 14.875 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_1_deg 6.203 r_lrange_it 4.4 r_lrange_other 4.166 r_scangle_it 3.141 r_scangle_other 3.118 r_scbond_it 2.263 r_scbond_other 2.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.268 r_dihedral_angle_4_deg 14.875 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_1_deg 6.203 r_lrange_it 4.4 r_lrange_other 4.166 r_scangle_it 3.141 r_scangle_other 3.118 r_scbond_it 2.263 r_scbond_other 2.224 r_angle_refined_deg 2.049 r_angle_other_deg 1.703 r_mcangle_it 1.658 r_mcangle_other 1.658 r_mcbond_it 1.151 r_mcbond_other 1.151 r_nbd_refined 0.251 r_symmetry_xyhbond_nbd_refined 0.229 r_xyhbond_nbd_refined 0.214 r_nbd_other 0.208 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.193 r_symmetry_nbd_refined 0.173 r_symmetry_xyhbond_nbd_other 0.137 r_chiral_restr 0.121 r_chiral_restr_other 0.111 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3470 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing