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The crystal structure of the catalytic domain of peptidoglycan N-acetylglucosamine deacetylase from Eubacterium rectale ATCC 33656
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1M Tris:HCl,
1.8M MgSO4
Crystal Properties Matthews coefficient Solvent content 2.24 45.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.495 α = 90 b = 60.323 β = 90 c = 79.577 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r Mirror 2016-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97933 APS 19-BM
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 1.54 33.42 99.7 0.131 20.3 6.7 33862 -3
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 1.54 1.57 97.4 0.85 1.7 4.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.54 33.42 1.34 33794 1694 99.58 0.157 0.1554 0.1611 0.1885 0.1884 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 f_dihedral_angle_d 13.965 f_angle_d 1.482 f_chiral_restr 0.078 f_bond_d 0.016 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1701 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 phasing HKL-3000 data reduction SBC-Collect data collection