8K1R
YeeE(TsuA)-YeeD(TsuB) complex for thiosulfate uptake
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 293 | 0.35 M Ammonium formate, 0.1M Tris-HCl pH 8.0-9.0, 26-36% 1,4- Butandiol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.47 | 64.51 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.58 | α = 90 |
b = 101.75 | β = 90 |
c = 182.76 | γ = 90 |
Symmetry | |
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Space Group | P 21 2 21 |
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 9M | 2023-06-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32XU | 1.0 | SPring-8 | BL32XU |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.6 | 49.93 | 99.52 | 0.9879 | 0.9893 | 0.0478 | 0.996 | 15.25 | 321.2 | 42977 | 31.95 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.6 | 2.693 | 99.32 | 5.227 | 5.236 | 0.2706 | 0.861 | 2.1 | 297.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 2.6 | 49.93 | 1.34 | 42847 | 1993 | 99.54 | 0.208 | 0.2059 | 0.2534 | 39.54 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 17.0138 |
f_angle_d | 1.1614 |
f_chiral_restr | 0.0484 |
f_bond_d | 0.0083 |
f_plane_restr | 0.0066 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6219 |
Nucleic Acid Atoms | |
Solvent Atoms | 108 |
Heterogen Atoms | 545 |
Software
Software | |
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Software Name | Purpose |
Coot | model building |
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |