Solution NMR Structure DE NOVO DESIGNED PFK fold PROTEIN, Northeast Structural Genomics Consortium (NESG) Target OR250
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 2 | 2D 1H-13C HSQC | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 3 | 3D HNCO | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 4 | 3D CBCA(CO)NH | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 5 | 3D HNCACB | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 6 | 3D 1H-13C arom NOESY | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 7 | 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 8 | 3D HCCH-TOCSY | 0.784 mM [U-100% 13C; U-100% 15N] OR250.001, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| 9 | 2D 1H-13C HSQC | 0.854 mM [U-100% 13C; U-100% 15N] OR250.003, 100 mM NaCl, 5 mM DTT, 0.02 % NaN3, 10 mM Tris-HCl pH 7.5 | 90% H2O/10% D2O | 6.5 | ambient | 298 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| 2 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| distance geometry, simulated annealing, torsion angle dynamics, molecular dynamics | CNS | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 2 | structure solution | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 3 | geometry optimization | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
| 4 | refinement | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
| 5 | geometry optimization | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
| 6 | structure solution | CYANA | 3.0 | Guntert, Mumenthaler and Wuthrich |
| 7 | data analysis | AutoStructure | 2.1 | Huang, Tejero, Powers and Montelione |
| 8 | refinement | AutoStructure | 2.1 | Huang, Tejero, Powers and Montelione |
| 9 | data analysis | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
| 10 | chemical shift assignment | AutoAssign | 2.1 | Zimmerman, Moseley, Kulikowski and Montelione |
| 11 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 12 | data analysis | XEASY | Bartels et al. | |
| 13 | peak picking | XEASY | Bartels et al. | |
| 14 | chemical shift assignment | XEASY | Bartels et al. | |
| 15 | collection | TopSpin | Bruker Biospin | |
| 16 | collection | VnmrJ | Varian | |
| 17 | data analysis | Sparky | Goddard | |
| 18 | geometry optimization | TALOS+ | Shen, Cornilescu, Delaglio and Bax | |
| 19 | structure validation | PSVS | Bhattacharya, Montelione | |
