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Crystal structure of Beta-glucuronidase from Escherichia coli in complex with siastatin B derived inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7PR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 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 49.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.281 α = 90 b = 76.711 β = 102.01 c = 141.018 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 2016-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979500 Diamond I02
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 1.95 67.04 98.4 0.997 8.1 4.1 94487
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 1.95 1.98 0.717
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 1.95 61.835 94471 4644 98.229 0.224 0.2206 0.2265 0.2847 0.2866 49.837
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] -1.065 -0.735 4.979 -3.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.386 r_dihedral_angle_3_deg 16.886 r_dihedral_angle_4_deg 14.877 r_dihedral_angle_1_deg 7.995 r_lrange_it 7.331 r_lrange_other 7.325 r_scangle_it 5.404 r_scangle_other 5.404 r_mcangle_it 5.337 r_mcangle_other 5.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.386 r_dihedral_angle_3_deg 16.886 r_dihedral_angle_4_deg 14.877 r_dihedral_angle_1_deg 7.995 r_lrange_it 7.331 r_lrange_other 7.325 r_scangle_it 5.404 r_scangle_other 5.404 r_mcangle_it 5.337 r_mcangle_other 5.337 r_mcbond_it 3.826 r_mcbond_other 3.826 r_scbond_it 3.666 r_scbond_other 3.666 r_angle_refined_deg 1.532 r_angle_other_deg 1.332 r_nbd_other 0.241 r_nbd_refined 0.208 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.196 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.128 r_symmetry_xyhbond_nbd_other 0.125 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9538 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing