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Crystal structure of Cutibacterium acnes exo-beta-1,4-mannosidase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 0.2 M MOPS buffer, 0.2 M magnesium acetate, 20% (w/v) PEG 8000 and 5 mM D-mannose
20 mM HEPES pH 7.5, 300 mM NaCl, 10% (v/v)glycerol, 0.5 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.76 55.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.18 α = 90 b = 104.37 β = 90.27 c = 112.75 γ = 90
Symmetry Space Group P 1 21 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 2017-02-09 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.07175 SOLEIL PROXIMA 1 2 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.03927 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.8 49.601 97.4 0.111 0.121 0.997 9.49 6.8 175603 26.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 96 0.0146 0.0159 0.74 1.92 6.7
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) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.8 49.601 1.35 175603 2001 97.46 0.1953 0.195 0.1956 0.2265 0.2267
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 7.429 f_angle_d 0.859 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12514 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 156
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling autoSHARP phasing ARP/wARP model building