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b-glucuronidase from Ruminococcus gnavus in complex with uronic deoxynojirimycin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 70% MPD, 0.1 M HEPES, pH 7.5, 0.2 M CaCl2
Crystal Properties Matthews coefficient Solvent content 2.54 51.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 162.501 α = 90 b = 103.331 β = 130.92 c = 112.213 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 277 CCD ADSC QUANTUM 210 2018-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 1 NSRRC BL13C1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 30 99.8 0.051 0.058 0.026 16.8 4.7 221212
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 99.6 0.49 0.561 0.27 0.814 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.502 28.384 1.33 217997 2000 98.06 0.1492 0.149 0.1694 0.1808 17.4136
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 f_dihedral_angle_d 13.533 f_angle_d 1.642 f_chiral_restr 0.112 f_bond_d 0.017 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9495 Nucleic Acid Atoms Solvent Atoms 1278 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing