2NAQ
3D NMR solution structure of NLRP3 PYD
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 | |
2 | 3D HNCACB | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 | |
3 | 3D CBCA(CO)NH | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 | |
4 | 3D HBHA(CO)NH | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 | |
5 | 3D H(CCO)NH | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 | |
6 | 3D HCCH-TOCSY | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 | |
7 | 3D 1H-15N NOESY | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 | |
8 | 3D 1H-13C NOESY | 100-200 uM [U-13C; U-15N] protein, 5 mM [U-2H] TCEP, 100 uM sodium azide | 95% H2O/5% D2O | 0.0051 | 3.6 | ambient | 303 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
DGSA-distance geometry simulated annealing | X-PLOR NIH |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | data analysis | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
4 | chemical shift assignment | PIPP | Garrett | |
5 | collection | TopSpin | Bruker Biospin | |
6 | data analysis | TALOS | Cornilescu, Delaglio and Bax | |
7 | data analysis | MOLMOL | Koradi, Billeter and Wuthrich | |
8 | geometry optimization | ProcheckNMR | Laskowski and MacArthur | |
9 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore |