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Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage phi24B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.9 M LiSO4, 10% [v/v] glycerol, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.37 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.522 α = 90 b = 54.824 β = 90 c = 72.77 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 315 2012-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.7514 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 0.97 25 99.5 0.079 0.99 14.64 7.1 128671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.97 0.98 1.55 0.4 1
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 0.97 24.49 1.35 128655 6441 99.5 0.1512 0.1501 0.1502 0.1719 0.172 15.71
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 14.0221 f_angle_d 0.9834 f_chiral_restr 0.0833 f_bond_d 0.0066 f_plane_restr 0.0055
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1615 Nucleic Acid Atoms Solvent Atoms 431 Heterogen Atoms 6
Software Software Software Name Purpose XDS data processing PHENIX refinement XDS data reduction XDS data scaling SHELXDE phasing