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beta-glucuronidase with an activity-based probe (N-alkyl cyclophellitol aziridine) bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VO0 PDB ENTRY 3VO0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.6 8.6
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.512 α = 90 b = 44.896 β = 114.78 c = 82.216 γ = 90
Symmetry Space Group C 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 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 42.6 99.5 0.05 12.1 4 59263 2.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99.5 0.59 2.2 4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3VO0 1.65 74.64 56355 2907 99.4 0.12289 0.12046 0.138 0.16922 0.1813 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.558 r_sphericity_free 30.578 r_dihedral_angle_4_deg 15.95 r_sphericity_bonded 13.36 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 9.191 r_long_range_B_refined 4.946 r_long_range_B_other 4.944 r_scangle_other 4.478 r_scbond_it 4.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.558 r_sphericity_free 30.578 r_dihedral_angle_4_deg 15.95 r_sphericity_bonded 13.36 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 9.191 r_long_range_B_refined 4.946 r_long_range_B_other 4.944 r_scangle_other 4.478 r_scbond_it 4.061 r_scbond_other 4.059 r_mcangle_other 3.422 r_mcangle_it 3.421 r_rigid_bond_restr 3.231 r_mcbond_it 2.823 r_mcbond_other 2.823 r_angle_refined_deg 1.859 r_angle_other_deg 1.308 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3428 Nucleic Acid Atoms Solvent Atoms 294 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing