3DWQ
Crystal structure of the A-subunit of the AB5 toxin from E. coli with Neu5Gc-2,3Gal-1,3GlcNAc
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.2 | 293 | 16% PEG 3350, 100mM sodium cacodylate, pH 6.2, 200mM ammonium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.18 | 61.34 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 97.253 | ¦Á = 90 |
b = 97.253 | ¦Â = 90 |
c = 163.52 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 65 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH3R |
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 | 2.1 | 84.22 | 45181 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 2.1 | 29.67 | 40527 | 2177 | 83.79 | 0.21338 | 0.21079 | 0.2615 | RANDOM | 23.623 |
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] | |
-1.04 | -0.52 | -1.04 | 1.56 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.821 |
r_dihedral_angle_3_deg | 13.501 |
r_dihedral_angle_4_deg | 7.757 |
r_dihedral_angle_1_deg | 5.97 |
r_angle_refined_deg | 1.538 |
r_scangle_it | 1.015 |
r_scbond_it | 0.589 |
r_mcangle_it | 0.535 |
r_mcbond_it | 0.304 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4532 |
Nucleic Acid Atoms | |
Solvent Atoms | 556 |
Heterogen Atoms | 292 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |