3CHB
CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2CHB | PDB ENTRY 2CHB |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | SITTING DROP, pH 7.0, vapor diffusion - sitting drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.79 | 31.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 102.124 | α = 90 |
b = 66.176 | β = 106.33 |
c = 78.221 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | 125 | IMAGE PLATE | MARRESEARCH | BENT CRYSTAL + VERTICAL MIRROR | 1997-02-01 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL7-1 | SSRL | BL7-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.25 | 40 | 92 | 0.031 | 11.9 | 3.1 | 126728 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.25 | 1.3 | 84 | 0.272 | 2.4 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | R-FREE | PDB ENTRY 2CHB | 1.25 | 22 | 123337 | 6491 | 92 | 0.1326 | 0.1326 | 0.18 | RANDOM |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
12 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.423 |
s_non_zero_chiral_vol | 0.073 |
s_anti_bump_dis_restr | 0.07 |
s_zero_chiral_vol | 0.065 |
s_approx_iso_adps | 0.046 |
s_similar_adp_cmpnt | 0.037 |
s_angle_d | 0.031 |
s_similar_dist | 0.016 |
s_bond_d | 0.013 |
s_rigid_bond_adp_cmpnt | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4098 |
Nucleic Acid Atoms | |
Solvent Atoms | 758 |
Heterogen Atoms | 347 |
Software
Software | |
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Software Name | Purpose |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX-96 | refinement |
CCP4 | data scaling |