2WT2
Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with tri(N-acetyl-lactosamine)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WSU | PDB ENTRY 2WSU, CHAIN A |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8 | 10 MM TRIS-HCL, 1 MM EDTA, 28% (W/V) POLY-ETHYLENE GLYCOL 3350, 300 MM LITHIUM NITRATE, 5 MM DITHIOTHREITOL, 5 MM TRI(N-ACETYL-LACTOSAMINE), PH 8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.9 | 36 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 176.13 | α = 90 |
b = 38.26 | β = 92.12 |
c = 86.52 | 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 | 100 | IMAGE PLATE | MAR555 FLAT PANEL | BENT, VERTICALLY FOCUSSING MIRROR | 2009-07-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | EMBL/DESY, HAMBURG BEAMLINE X11 | EMBL/DESY, HAMBURG | X11 |
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 | 2.5 | 40 | 99.9 | 0.1 | 8.8 | 3.6 | 20441 | 2 | 44.8 |
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 | 2.5 | 2.64 | 99.8 | 0.43 | 3.1 | 3.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | PDB ENTRY 2WSU, CHAIN A | 2.5 | 35 | 19313 | 1123 | 100 | 0.20365 | 0.19989 | 0.2679 | THIN SHELLS | 26.572 |
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] | |
-1.01 | -0.34 | -2.17 | 3.15 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.914 |
r_dihedral_angle_4_deg | 14.491 |
r_dihedral_angle_3_deg | 13.329 |
r_dihedral_angle_1_deg | 6.902 |
r_scangle_it | 4.226 |
r_mcangle_it | 2.95 |
r_scbond_it | 2.906 |
r_mcbond_it | 1.875 |
r_angle_refined_deg | 1.274 |
r_angle_other_deg | 0.783 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4708 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms | 176 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |