3F2E
Crystal structure of Yellowstone SIRV coat protein C-terminus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 299 | SIRV CP (residues 46-134) at 19 or 30 mg/ml in 20 mM Na MES pH 6.0 was mixed 1:1 with 25% PEG 20,000, 0.1 M Na Citrate pH 3.6, 4-9% sucrose. Crystals were frozen in of 14% PEG 20,000, 50 mM sodium citrate pH 3.6, 15-25% sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 299K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.74 | 55.14 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.41 | α = 90 |
b = 54.41 | β = 90 |
c = 77.79 | γ = 90 |
Symmetry | |
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Space Group | P 43 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 | 173 | IMAGE PLATE | MAR scanner 345 mm plate | 2008-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-D | 1.542 |
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 | 1.668 | 44.588 | 99.1 | 0.034 | 0.062 | 33.4 | 16.8 | 14062 | -3 | 24.675 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.668 | 1.7 | 94.6 | 0.203 | 0.371 | 8.27 | 14.5 | 965 |
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-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | CS-Rosetta model | 1.668 | 31.642 | 2 | 14055 | 703 | 99.04 | 0.1846 | 0.1837 | 0.2018 | random | 20.5 |
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] | |
-0.2583 | -0.2583 | -5.774 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.532 |
f_angle_deg | 0.833 |
f_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 600 |
Nucleic Acid Atoms | |
Solvent Atoms | 80 |
Heterogen Atoms | 13 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |