4IND
The Triple Jelly Roll Fold and Turret Assembly in an Archaeal Virus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 291 | 10 mg/mL native protein, 0.1 M sodium phosphate/citric acid, pH 4.2, 30-40% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
2 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 291 | 10 mg/mL Se-Met protein, 0.1 M sodium phosphate/citric acid, pH 4.2, 30-40% PEG600, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.774 | α = 81.84 |
b = 166.999 | β = 82.17 |
c = 186.975 | γ = 81.44 |
Symmetry | |
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Space Group | P 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 | PIXEL | DECTRIS PILATUS 6M | Shutterless data collection, fine phi slicing experiments | 2012-08-09 | M | SINGLE WAVELENGTH | |||||
2 | 2 | x-ray | 100 | CCD | MARMOSAIC 325 mm CCD | Sample to detector distance: 100 to 650 mm, Maximum vertical offset: 200 mm | 2011-06-25 | M | SAD |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL12-2 | 0.95369 | SSRL | BL12-2 |
2 | SYNCHROTRON | SSRL BEAMLINE BL9-2 | 0.97893 | SSRL | BL9-2 |
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 | 1.76 | 39.19 | 88 | 0.123 | 0.038 | 6.4 | 3.6 | 951878 | 837015 | 1.06 | 0.34 | 29.29 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1,2 | 1.76 | 1.86 | 63.9 | 0.4 | 3.4 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | 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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | 1.8 | 39.186 | 1.96 | 774229 | 38896 | 86.87 | 0.195 | 0.1898 | 0.1883 | 0.2166 | RANDOM | 39.3211 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 12.128 |
f_angle_d | 1.18 |
f_chiral_restr | 0.084 |
f_bond_d | 0.009 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 58460 |
Nucleic Acid Atoms | |
Solvent Atoms | 4520 |
Heterogen Atoms | 300 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
Blu-Ice | data collection |
XDS | data reduction |
SCALA | data scaling |
PHENIX | phasing |