7AK7
Structure of Salmonella TacT2 toxin bound to TacA2 antitoxin
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5FVJ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 277 | 0.01M Magnessium chloride hexahydrate 0.05M MES monohydrate 1.8M Lithium sulfate monohydrate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.19 | 43.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 49.491 | α = 100.57 |
b = 54.452 | β = 97.73 |
c = 76.9 | γ = 117 |
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 EIGER X 16M | 2019-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.14 | 73.22 | 97.1 | 0.073 | 0.103 | 0.073 | 0.992 | 3.8 | 1.8 | 36519 | 29.113 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.14 | 2.18 | 92.2 | 0.726 | 0.514 | 1.2 | 1.8 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 5FVJ | 2.14 | 46.66 | 34696 | 1795 | 97.07 | 0.2219 | 0.2197 | 0.2634 | RANDOM | 37.95 |
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] | |
0.04 | -0.01 | 0.05 | -0.05 | 0.04 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 28.416 |
r_dihedral_angle_4_deg | 17.916 |
r_dihedral_angle_3_deg | 15.942 |
r_dihedral_angle_1_deg | 6.554 |
r_angle_refined_deg | 1.385 |
r_angle_other_deg | 1.265 |
r_chiral_restr | 0.063 |
r_bond_refined_d | 0.007 |
r_gen_planes_refined | 0.005 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4823 |
Nucleic Acid Atoms | |
Solvent Atoms | 321 |
Heterogen Atoms | 103 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data scaling |
PDB_EXTRACT | data extraction |
xia2 | data reduction |
PHASER | phasing |