8DOP
Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P1 Form)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 291 | Morpheus B4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM NaF, 30 mM NaBr and 30 mM NaI, KlaeA.01229.a.B1 at 15 mg/mL with 2.5 GDP added. No electron density for GDP was observed, Tray: plate 12527 well B4 drop 3, Puck: PSL0811, Cryo: DIRECT |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.94 | 36.46 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 69.021 | α = 108.39 |
b = 71.159 | β = 102.23 |
c = 93.183 | γ = 89.99 |
Symmetry | |
---|---|
Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 XE 9M | 2022-04-08 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | PIXEL | Bruker PHOTON III | Helios Multilayer | 2022-03-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS-II BEAMLINE 19-ID | 0.97949 | NSLS-II | 19-ID |
2 | SEALED TUBE | BRUKER D8 QUEST | 1.54184 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 49.41 | 97.6 | 0.059 | 0.998 | 12.2 | 3.6 | 108150 | 33.37 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.03 | 96.9 | 0.607 | 0.758 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | SAD | THROUGHOUT | 2 | 49.41 | 1.18 | 108138 | 5279 | 97.55 | 0.1903 | 0.1875 | 0.2458 | 41.4744 |
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 | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 12802 |
Nucleic Acid Atoms | |
Solvent Atoms | 390 |
Heterogen Atoms | 18 |
Software
Software | |
---|---|
Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
CRANK2 | phasing |