SOLUTION NMR

NMR Experiment
Experiment Type Sample Contents Ionic Strength Solvent pH Pressure Temprature (K)
1 2D 1H-1H NOESY 2 mM control DNA duplex, 95% H2O/5% D2O 70 95% H2O/5% D2O 7.0-7.2 ambient 298
2 2D 1H-1H TOCSY 2 mM control DNA duplex, 95% H2O/5% D2O 70 95% H2O/5% D2O 7.0-7.2 ambient 298
3 2D DQF-COSY 2 mM control DNA duplex, 95% H2O/5% D2O 70 95% H2O/5% D2O 7.0-7.2 ambient 298
4 2D DQF-COSY 2 mM control DNA duplex, 95% H2O/5% D2O 70 95% H2O/5% D2O 7.0-7.2 ambient 298
5 2D 1H-13C HSQC 2 mM control DNA duplex, 95% H2O/5% D2O 70 95% H2O/5% D2O 7.0-7.2 ambient 298
NMR Spectrometer Information
Spectrometer Manufacturer Model Field Strength
NMR Refinement
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. 1
NMR Ensemble Information
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
# Classification Version Software Name Author
1 collection 2.1B VnmrJ Varian
2 processing 4.9 NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3 chemical shift assignment 8.0.b30 NMRView Johnson, One Moon Scientific
4 noe calibration ? MARDIGRAS T.L. James
5 structure solution 10 Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
6 refinement 10 Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
7 structure validation ? CORMA T.L. James