6WM5
Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | LIPIDIC CUBIC PHASE | 6 | 295 | 100 mM Sodium citrate, pH 6, 50 mM sodium chloride, 20 mM magnesium chloride hexahydrate, 22% PEG 400 (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein (Sigma) in a 1:1.5 protein to lipid ratio (w/w). Monoolein was doped with 2% CDP-DAG |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.81 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.338 | α = 90 |
b = 60.241 | β = 90.91 |
c = 85.377 | 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 16M | MD2 diffractometer | 2017-02-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 0.9791 | APS | 24-ID-E |
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 | 1.96 | 49.22 | 66 | 0.1061 | 0.1501 | 0.1061 | 0.989 | 6.23 | 1.9 | 37482 | 25.57 |
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 | 1.96 | 2.037 | 3.27 | 0.64 | 0.9051 | 0.64 | 0.11 | 0.98 |
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 | 5D91,4O6M | 1.961 | 49.22 | 1.33 | 37478 | 1930 | 65.38 | 0.2369 | 0.2347 | 0.277 | 33.7529 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5025 |
Nucleic Acid Atoms | |
Solvent Atoms | 103 |
Heterogen Atoms | 460 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |
STARANISO | data scaling |
PARROT | phasing |
PHENIX | refinement |
Coot | model building |
PDB_EXTRACT | data extraction |