2WBV
Canine adenovirus 2 fibre head in complex with sialic acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J2J | PDB ENTRY 2J2J |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5% PEG 4000, 5% ISOPROPANOL, 0.1 M HEPES PH 7.4 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.54 | 51.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 215 | α = 90 |
b = 61.25 | β = 131.67 |
c = 143.11 | 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 | CCD | ADSC QUANTUM | 2005-09-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID29 | ESRF | ID29 |
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 | 1.9 | 46.1 | 99.4 | 0.15 | 10.22 | 3.7 | 109731 | 1 |
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 | 1.9 | 1.97 | 98.8 | 0.4 | 4.06 | 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 2J2J | 1.9 | 46.13 | 104251 | 5480 | 99.8 | 0.159 | 0.157 | 0.195 | RANDOM | 9.16 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.06 | -0.07 | 0.19 | -0.22 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.773 |
r_dihedral_angle_4_deg | 11.829 |
r_dihedral_angle_3_deg | 11.407 |
r_dihedral_angle_1_deg | 6.786 |
r_scangle_it | 2.253 |
r_scbond_it | 1.373 |
r_angle_refined_deg | 1.266 |
r_mcangle_it | 0.963 |
r_angle_other_deg | 0.847 |
r_mcbond_it | 0.602 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8493 |
Nucleic Acid Atoms | |
Solvent Atoms | 1152 |
Heterogen Atoms | 173 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHASER | phasing |