7NLI
S. cerevisiae Ty1 p22 restriction factor, Gag CA-CTD, AUG2 variant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 291 | 260 nL Protein (13.6 mg/ml in 50 mM Sodium Acetate pH 5.0, 300 mM NaCl 1mM TCEP) 120 nL Mother Liquor (27.9% Glycerol, 17.7% PEG 4K 0.1M HEPES pH 7.5) 20 nL Seed solution (seeds in 20% Glycerol, 31% PEG 4K 0.1M HEPES pH 7.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
6.42 | 80.86 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 280.89 | α = 90 |
b = 280.89 | β = 90 |
c = 40.405 | γ = 120 |
Symmetry | |
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Space Group | P 65 2 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 | 100 | PIXEL | DECTRIS PILATUS 6M-F | 2018-03-08 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97928, 0.97943, 0.97281 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | 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 | 3.119 | 140.45 | 100 | 0.246 | 0.983 | 24.5 | 112.8 | 31760 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 3.119 | 3.33 | 100 | 1.313 | 0.167 | 0.76 | 6.8 | 115.8 |
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 | MAD | THROUGHOUT | Ty1 p22 | 3.119 | 91.943 | 2.46 | 31754 | 1663 | 99.93 | 0.2346 | 0.2334 | 0.2578 | Matches related structures | 94.9444 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2203 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
REFMAC | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |
DIALS | data reduction |
Aimless | data scaling |
SHELXDE | phasing |