6VHD
FphF, Staphylococcus aureus fluorophosphonate-binding serine hydrolases F, KT129 bound
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 289.15 | 0.2 uL ~7.5 mg/ml FphF+KT129 (0.12mM KT129, 12% DMSO, 18 mM HEPES pH 7.5, 8 mM NaCl) were mixed with 0.2 uL of reservoir solution. Sitting drop reservoir contained 50 uL of 0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350. Crystals were soaked for ~20 seconds in 75% reservoir solution and 25% glycerol prior to freezing in liquid nitrogen |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.48 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 87.202 | α = 90 |
b = 87.202 | β = 90 |
c = 455.197 | γ = 120 |
Symmetry | |
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Space Group | P 61 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 EIGER X 16M | 2019-07-31 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.954 | Australian Synchrotron | MX2 |
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 | 1.98 | 49.28 | 99.9 | 0.151 | 0.154 | 0.029 | 0.999 | 16.7 | 27.1 | 73040 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.98 | 2.02 | 98.5 | 2.676 | 2.73 | 0.535 | 0.711 | 24.9 |
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 | 6VH9 | 1.98 | 49.28 | 1.91 | 72838 | 6711 | 99.86 | 0.178 | 0.1761 | 0.2131 | 46.9353 |
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 | 8236 |
Nucleic Acid Atoms | |
Solvent Atoms | 258 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |