Solution structure for the protein coded by gene locus BB0938 of Bordetella bronchiseptica. Northeast Structural Genomics target BoR11.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_13C-separated_NOESY | 0.7mM BoR11 (U-13C,15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5 | 5% D2O, 95% H2O | 100 mM NaCl | 6.5 | atmospheric atm | 293 | |
| 2 | 3D_15N-separated_NOESY | 0.7mM BoR11 (U-13C,15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5 | 5% D2O, 95% H2O | 100 mM NaCl | 6.5 | atmospheric atm | 293 | |
| 3 | 4D_13C-separated_NOESY | 0.5mM BoR11 (U-13C,15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5 | 99.9% D2O | 100 mM NaCl | 6.5 | atmospheric atm | 293 | |
| 4 | HNCA-J | 0.8mM BoR11 (5% 13C,U-15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5 | 5% D2O, 95% H2O | 100 mM NaCl | 6.5 | atmospheric atm | 293 | |
| 5 | Hi-Res 13C-HSQC for VL stereospecific | 0.8mM BoR11 (5% 13C,U-15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5 | 5% D2O, 95% H2O | 100 mM NaCl | 6.5 | atmospheric atm | 293 | |
| 6 | het-NOE | 0.8mM BoR11 (5% 13C,U-15N), 0.02% NaN3, 10mM DTT, 5mM CaCl2, 100mM NaCl, 20mM MES, pH 6.5 | 5% D2O, 95% H2O | 100 mM NaCl | 6.5 | atmospheric atm | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Varian | INOVA | 750 |
| 3 | Varian | INOVA | 800 |
| 4 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| CS assignment: Backbone AutoAssign, manual sidechain HcCH-COSY and TOCSYs. AutoStructure for noesy assign. Hyper Dihedral, Dyana, Xplor(nih), and CNS force-field for simulated annealing (Dyana,xplor run within AutoStructure GUI) | VNMR | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 56 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest target function) |
| Additional NMR Experimental Information | |
|---|---|
| Details | AutoQF scores after CNS with explicit H2O refinement: final M-score: 0.188 final dp-score: 0.73 (recall=0.986, precision=0.857, F-measure=0.917) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1c | Varian Inc. |
| 2 | collection | XwinNMR | 3.5 | Bruker Biospin AG |
| 3 | data analysis | NMRPipe | 2.1 | Delaglio |
| 4 | structure solution | AutoStructure | 2.1.1 | Huang, Montelione |
| 5 | data analysis | AutoAssign | 1.15 | Zimmerman, Moseley, Montelione |
| 6 | data analysis | Sparky | 3.91 | Goddard |
| 7 | refinement | CNS | 1.1 | Brunger |
| 8 | structure solution | xplor(nih) | 2.0.6 | Schwieters, Clore |
| 9 | structure solution | DYANA | 1.5 | Guntert |
