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Crystal structure of E. coli beta-glucuronidase in complex with covalent inhibitor ME727
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M Bis-Tris propane pH 7.5, 20% (w/v) PEG 3350, 0.2 M NaNO3
Crystal Properties Matthews coefficient Solvent content 2.44 49.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.8 α = 90 b = 76.58 β = 125.01 c = 125.74 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 EIGER2 XE 16M 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97933 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.99 47.76 97.3 0.139 0.083 0.983 6.5 3.9 86916
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.04 98.7 1.695 0.983 0.334 0.8 3.9
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 3k46 1.99 47.803 86915 4333 96.893 0.223 0.2209 0.226 0.2631 0.2645 48.325
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] -1.766 -0.283 1.572 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.678 r_dihedral_angle_4_deg 15.514 r_dihedral_angle_3_deg 14.33 r_dihedral_angle_1_deg 8.092 r_lrange_it 5.012 r_lrange_other 4.98 r_scangle_it 3.637 r_scangle_other 3.636 r_mcangle_it 3.06 r_mcangle_other 3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.678 r_dihedral_angle_4_deg 15.514 r_dihedral_angle_3_deg 14.33 r_dihedral_angle_1_deg 8.092 r_lrange_it 5.012 r_lrange_other 4.98 r_scangle_it 3.637 r_scangle_other 3.636 r_mcangle_it 3.06 r_mcangle_other 3.06 r_angle_other_deg 2.368 r_scbond_it 2.321 r_scbond_other 2.321 r_mcbond_it 2.005 r_mcbond_other 2.005 r_angle_refined_deg 1.716 r_symmetry_nbd_refined 0.281 r_nbd_other 0.273 r_symmetry_nbd_other 0.226 r_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.064 r_bond_other_d 0.035 r_gen_planes_other 0.016 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9566 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing