2KD4 | pdb_00002kd4

Solution structure and thermodynamics of 2',5' RNA intercalation

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	1H-1H NOESY	2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4	99.9% D2O	260	6.5	1 atm	282
2	31P-1H HETCOR	2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4	99.9% D2O	260	6.5	1 atm	282
3	1H-1H TOCSY	2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4	99.9% D2O	260	6.5	1 atm	282
4	31P-decoupled 1H-1H COSY	2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4	99.9% D2O	260	6.5	1 atm	282
5	1H-1H NOESY with WATERGATE water suppression	2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4	99.9% D2O	130		1 atm	282

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600
2	Bruker	DRX	500

NMR Refinement
Method	Details	Software
simulated annealing	300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	10
Conformers Submitted Total Number	1
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR		Bruker Biospin
2	data analysis	XwinNMR		Bruker Biospin
3	processing	XwinNMR		Bruker Biospin
4	chemical shift assignment	Sparky		Goddard
5	data analysis	Sparky		Goddard
6	structure solution	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
7	refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm