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Vibrio Cholerae Cytolysin Beta-Prism Domain With Methyl-Alpha-Mannose Bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XEZ PDB Entry 1XEZ (Residues 585-716)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.1 M ammonium acetate, 0.1 M Bis-tris, 25% PEG 3350, 30 mM Me-alpha-mannose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.77 α = 90 b = 99.77 β = 90 c = 172.366 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 OXFORD ONYX CCD 2012-01-30 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.85 24.895 99.8 0.211 7.1 4.9 23789 23789
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 100 0.477 0.477 1.5 4.9 3401
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 MOLECULAR REPLACEMENT PDB Entry 1XEZ (Residues 585-716) 2.85 24.895 1.35 23763 1182 99.95 0.1973 0.1946 0.1962 0.2481 0.248 RANDOM 24.7374
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 14.392 f_angle_d 1.045 f_chiral_restr 0.058 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5775 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 78
Software Software Software Name Purpose d*TREK data scaling SCALA data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction d*TREK data reduction