2GVO | pdb_00002gvo

Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM	6.8	ambient	274
2	2D NOESY	1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM	6.8	ambient	298
3	3D HCCH-COSY	1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM	6.8	ambient	298
4	2D 1H-13C HSQC	1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM	6.8	ambient	298
5	DQF-COSY	1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM	6.8	ambient	298
6	HNN COSY	1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O	90% H2O/10% D2O	10mM	6.8	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500

NMR Refinement
Method	Details	Software
molecular dynamics	the structures are based on a total of 187 restraints, 84 are sequential and long range internucleotide distances, 85 dihedral angle restraints, 18 sugar puckers restraints and 15 distance restaints from hydrogen bonds.	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy,structures with the least restraint violations, structures with the lowest energy
Conformers Calculated Total Number	30
Conformers Submitted Total Number	21
Representative Model	1 (n/a)

Additional NMR Experimental Information
Details	The structure was determined using triple-resonance NMR spectroscopy

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	NMRPipe	2.2	Delaglio, F. et al.
2	data analysis	Sparky	3.110	Goddard, T.D., Kneller, G.D.
3	data analysis	Felix	97.0
4	structure solution	Amber	7.0	Case, D.A. et al.'
5	structure solution	JUMNA	12	Lavery, R., Zakrzewska, K., Sklenar, H
6	refinement	Amber	7	CASE, D.A. et al.