1JVE | pdb_00001jve

NMR Structure of an AT-Rich DNA with the GAA-Hairpin Loop

SOLUTION NMR

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NMR Experiment
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
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600

NMR Refinement
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
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
Details	This structure was determined using standard 2D homonuclear techniques.

Computation: NMR Software
#	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.