NMR structure of the E.coli protein NirD, Northeast Structural Genomics target ET100
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D 1H-15N NOESY | 1 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide | 95% H2O/5% D2O | 300 | 7.0 | ambient | 293 | |
| 2 | 2D 1H-15N HSQC | 1 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide | 95% H2O/5% D2O | 300 | 7.0 | ambient | 293 | |
| 3 | 2D 1H-13C HSQC | 1 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide | 95% H2O/5% D2O | 300 | 7.0 | ambient | 293 | |
| 4 | 3D HNCACB | 1 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide | 95% H2O/5% D2O | 300 | 7.0 | ambient | 293 | |
| 5 | 3D 1H-13C NOESY | 1 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide | 95% H2O/5% D2O | 300 | 7.0 | ambient | 293 | |
| 6 | 4D CC NOESY | 1 mM [U-100% 13C] protein, 10 mM TRIS, 300 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide | 100% D2O | 300 | 7.0 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Varian | INOVA | 750 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | simulated annealing using NIH xplor, followed by cns water refinement. | AutoStructure |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 25 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | data analysis | AutoStructure | 2.1.1 | Huang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelione |
| 2 | structure solution | X-PLOR NIH | 2.15.0 | Schwieters, Kuszewski, Tjandra and Clore |
| 3 | refinement | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 4 | peak picking | Sparky | 3.1 | Goddard |
| 5 | processing | NMRPipe | linux9 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
