3WE1
Crystal structure of Dengue 4 Envelope protein domain III (ED3)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3AUJ | PDB ENTRY 3AUJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 277 | 30.0% PEG 3350, 0.2M Ammonium sulphate, 0.1M Tris-HCl pH 8.5, 1% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.32 | 63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 91.38 | α = 90 |
b = 91.38 | β = 90 |
c = 73.109 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 | 195 | CCD | ADSC QUANTUM 315r | Mono-chromator 17.5 m Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Vertical Focusing Mirror 22.22 m Rhodium coated silicon single crystal (Flat shaped, 1000 mm (L) x 100 mm (W) x 50 mm (T) ) with 4.0 mrad glancing angle. Horizontal Focusing Mirror 29.5 m Rhodium coated silicon single crystal (Flat shaped, 1000 mm (L) x 100 mm (W) x 40 mm (T) ) with 4.0 mrad glancing angle. | 2012-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.98 | Photon Factory | BL-17A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 2.27 | 10 | 100 | 0.064 | 0.2669 | 29.07 | 13.6 | 14490 | 3 | 33.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 3AUJ | 2.278 | 9.967 | 1.34 | 14456 | 732 | 99.94 | 0.2669 | 0.2669 | 0.2657 | 0.2897 | 37.76 |
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] | |
-2.9864 | -2.9864 | 5.9728 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.063 |
f_angle_d | 1.132 |
f_chiral_restr | 0.069 |
f_bond_d | 0.008 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1461 |
Nucleic Acid Atoms | |
Solvent Atoms | 117 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHENIX | model building |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |