6UPC
Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose 6-sulfate
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 290 | Drop Contained: 2 uL 40 mg/mL protein, 2 uL reservoir solution (19% PEG 3350, 375 mM lithium citrate, 10 mM magnesium chloride 2% 1,4 dioxane) and 0.5 uL 1:10^9 dilution of seed stock prepared according to the Seed Bead protocol. Crystals were transferred to a drop containing 24% PEG 3350, 50 mM lithium citrate, 100 mM magnesium chloride, 10% ethylene glycol and 5 mM trehalose 6-phosphate for 1 hours prior to cryocooling |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.16 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.525 | α = 90 |
b = 52.639 | β = 99.23 |
c = 107.053 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 9M | 2018-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 17-ID-1 | 0.9201 | NSLS-II | 17-ID-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.505 | 29.273 | 99.2 | 0.075 | 0.993 | 8.03 | 2 | 17698 | 41.15 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.505 | 2.595 | 94.69 | 0.4797 | 0.616 |
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 | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6UPB | 2.505 | 29.273 | 1.35 | 17696 | 1768 | 99.22 | 0.1969 | 0.1934 | 0.2277 | 51.4037 |
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 | 3772 |
Nucleic Acid Atoms | |
Solvent Atoms | 85 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |