4GX7
Vibrio Cholerae Cytolysin Beta-Prism Domain With Methyl-Alpha-Mannose Bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1XEZ | PDB Entry 1XEZ (Residues 585-716) |
Crystallization
Crystalization Experiments | ||||
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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 | |
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Matthews coefficient | Solvent content |
2.53 | 51.42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.77 | α = 90 |
b = 99.77 | β = 90 |
c = 172.366 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OTHER | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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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 | |||||||||||||||||||
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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 | R-Free | 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 | 0.2481 | 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 | |
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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 | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5775 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
SCALA | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |