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Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.6 288 6% (w/v) polyethylene glycol 4000, 0.1 M sodium acetate trihydrate (pH 4.6)
Crystal Properties Matthews coefficient Solvent content 3.28 62.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.725 α = 90 b = 102.725 β = 90 c = 118.653 γ = 120
Symmetry Space Group P 31 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 CCD ADSC QUANTUM 210 2015-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.903 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.49 24.16 99.6 37.59 16.8 117632
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 FREE R-VALUE 1.49 24.157 1.52 117632 5896 99.63 0.1351 0.134 0.1555 0.1624
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 12.707 f_angle_d 1.268 f_chiral_restr 0.071 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3857 Nucleic Acid Atoms Solvent Atoms 759 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing Coot model building