3FBM
D431N Mutant VP2 Protein of Infectious Bursal Disease Virus; Derived T=1 Particles
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2GSY | PDB ENTRY 2GSY |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 9 | 293 | 14-17% PEG 4000, 0.1M TRIS pH 9.0, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
50.03 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 326.725 | α = 90 |
b = 326.725 | β = 90 |
c = 326.725 | 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 | 100 | CCD | ADSC QUANTUM 4 | 2007-06-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | 0.933 | ESRF | ID14-2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 3.1 | 50 | 99 | 0.12 | 9.3 | 5.3 | 208686 | 206393 | 3 | 3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 3.1 | 3.27 | 95.8 | 1.9 | 4.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2GSY | 3.1 | 20 | 10000 | 3 | 189714 | 187105 | 9151 | 90 | 0.301 | 0.294 | 0.294 | 0.291 | RANDOM | 35.4 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 25.8 |
c_scangle_it | 2.99 |
c_mcangle_it | 2.68 |
c_scbond_it | 1.91 |
c_mcbond_it | 1.47 |
c_angle_deg | 1.4 |
c_improper_angle_d | 0.9 |
c_bond_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3209 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
REFMAC | refinement |
CNS | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
REFMAC | phasing |