1JVE
NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D-NOESY | 2mM DNA; phosphate buffer: 30 mM K+; 1mM EDTA | 90% H2O/10% D2O | 30 mM K+ | 8.0 | ambient | 283 | |
2 | DQF-COSY | 2mM DNA; phosphate buffer: 30 mM K+; 1mM EDTA | 90% H2O/10% D2O | 30 mM K+ | 8.0 | ambient | 283 | |
3 | TOCSY | 2mM DNA; phosphate buffer: 30 mM K+; 1mM EDTA | 90% H2O/10% D2O | 30 mM K+ | 8.0 | ambient | 283 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
full matrix relaxation analysis of NOE, random error analysis of NOE, simulated annealing using torsion angle dynamics, simulated annealing using Metropolis Monte Carlo, restrained minimization | The NMR refinement was based on a total of 434 interproton distance restraints (16.1 per residue). The restraints include 353 MARDIGRAS-derived quantitative restraints for nonexchangeable protons (with an average flat-well width of 1.51 angstroms), 63 qualitative restraints for exchangeable protons, and 18 H-bond restraints for Watson-Crick GC pairs. | VNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | Lowest target function (a weighted sum of conformational energy and restraint energy). |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | VNMR | 6.1 | Varian Associates, Inc. |
2 | processing | NMRPipe | 1.8 | Delaglio, F. |
3 | data analysis | Sparky | 3.1 | Goddard, T.D., Kneller, D.G. |
4 | iterative matrix relaxation | MARDIGRAS | 3.2 | Borgias, B.A., Thomas, P.D., Liu, H., Kumar, A., Tonelli, M. |
5 | refinement | DYANA | 1.5 | Guntert, P. |
6 | refinement | miniCarlo | alpha version | Ulyanov, N.B., Gorler, A., Gorin, A.A., Zhurkin, V.B. |