2L8Q
Solution Structure of a control DNA Duplex
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 2 mM control DNA duplex | 95% H2O/5% D2O | 70 | 7.0-7.2 | ambient | 298 | |
2 | 2D 1H-1H TOCSY | 2 mM control DNA duplex | 95% H2O/5% D2O | 70 | 7.0-7.2 | ambient | 298 | |
3 | 2D DQF-COSY | 2 mM control DNA duplex | 95% H2O/5% D2O | 70 | 7.0-7.2 | ambient | 298 | |
4 | 2D DQF-COSY | 2 mM control DNA duplex | 95% H2O/5% D2O | 70 | 7.0-7.2 | ambient | 298 | |
5 | 2D 1H-13C HSQC | 2 mM control DNA duplex | 95% H2O/5% D2O | 70 | 7.0-7.2 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 500 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The upper bounds obtained from MARDIGRAS were multiplied by a factor 1.25 before being exported to Amber 10 for a 25 ps simulated annealing protocol. The simulated annealing protocol using the pairwise generalized Born model was as follows: the temperature of the system was kept constant at 600 K during the first 5 ps, cooled down slowly to 100 K between 5-18 ps, and cooled down to 0 K for the last 7 ps. The protocol was repeated 50 times to obtain an NMR ensemble with the 10 lowest RMSD structures. The structure with the lowest RMSD of the ensemble was put back into MARDIGRAS for a second and third cycle of NOE calibration and structure calculations. | VnmrJ |
NMR Ensemble Information | |
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Conformer Selection Criteria | lowest RMSD to average structure |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | VnmrJ | 2.1B | Varian |
2 | processing | NMRPipe | 4.9 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
3 | chemical shift assignment | NMRView | 8.0.b30 | Johnson, One Moon Scientific |
4 | noe calibration | MARDIGRAS | T.L. James | |
5 | structure solution | Amber | 10 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
6 | refinement | Amber | 10 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
7 | structure validation | CORMA | T.L. James |