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beta-glucuronidase with an activity-based probe (N-acyl 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 8.6 293 0.7 UL 4.5 MG/ML PROTEIN STOCK IS MIXED WITH 0.5 UL PRECIPITANT COMPOSED OF 1 M NAH2PO4:K2HPO4 = 0.5:9.5 (V/V) AT 20 DEGREE., pH 8.6
Crystal Properties Matthews coefficient Solvent content 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.74 α = 90 b = 44.81 β = 115.5 c = 83.27 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 2014-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.8 66.71 98 0.07 13.6 4.1 45856 2.1
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 1.8 1.85 98 0.54 2.1 2.1
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 (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 1.8 66.71 43578 2278 97.66 0.18412 0.1826 0.1926 0.21319 0.2212 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 33.713 r_dihedral_angle_4_deg 14.712 r_dihedral_angle_3_deg 13.558 r_dihedral_angle_1_deg 6.331 r_long_range_B_other 4.87 r_long_range_B_refined 4.86 r_scangle_other 3.441 r_mcangle_it 2.385 r_mcangle_other 2.385 r_scbond_it 2.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.713 r_dihedral_angle_4_deg 14.712 r_dihedral_angle_3_deg 13.558 r_dihedral_angle_1_deg 6.331 r_long_range_B_other 4.87 r_long_range_B_refined 4.86 r_scangle_other 3.441 r_mcangle_it 2.385 r_mcangle_other 2.385 r_scbond_it 2.226 r_scbond_other 2.213 r_angle_refined_deg 1.812 r_mcbond_it 1.583 r_mcbond_other 1.579 r_angle_other_deg 1.066 r_chiral_restr 0.112 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3430 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing