2CAU
CANAVALIN FROM JACK BEAN
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1CAV | PDB ENTRY 1CAV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.8 | THIS CRYSTAL FORM COULD BE GROWN ONLY OCCASIONALLY. BASICALLY IT WAS CRYSTALLIZED FROM PURIFIED PROTEIN AFTER TRYPSIN TREATMENT IN PHOSPHATE BUFFERED SALINE, BUT WAS DIFFICULT TO REPRODUCE., pH 6.8 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 105.99 | α = 90 |
b = 105.99 | β = 90 |
c = 105.99 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 | 291 | AREA DETECTOR | SDMS | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 |
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 | 2.02 | 40 | 85.5 | 0.048 | 21 | 3.2 | 22331 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.02 | 2.18 | 66.5 | 0.184 | 3 | 1.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1CAV | 2.1 | 40 | 2 | 19695 | 1523 | 84 | 0.175 | 0.235 | RANDOM | 28.3 |
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 |
x_dihedral_angle_d | 27.8 |
x_scangle_it | 4.51 |
x_scbond_it | 2.8 |
x_mcangle_it | 2.52 |
x_angle_deg | 1.569 |
x_mcbond_it | 1.52 |
x_improper_angle_d | 0.729 |
x_bond_d | 0.01 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2764 |
Nucleic Acid Atoms | |
Solvent Atoms | 101 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
MERLOT | phasing |
X-PLOR | refinement |
SDMS | data reduction |
SDMS | data scaling |