5V2R | pdb_00005v2r

Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3')	95% H2O/5% D2O	0.1 M	6.2	ambient	273	Varian INOVA 600
2	2D 1H-1H TOCSY	3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3')	95% H2O/5% D2O	0.1 M	6.2	ambient	273	Varian INOVA 600
3	2D 1H-1H NOESY	3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3')	100% D2O	0.1 M	6.2	ambient	283	Varian INOVA 600
4	2D 1H-1H TOCSY	3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3')	100% D2O	0.1 M	6.2	ambient	283	Varian INOVA 600
5	2D 31P-1H COSY	3.1 mM None RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3')	100% D2O	0.1 M	6.2	ambient	283	Varian INOVA 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest restraint energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	33
Representative Model	1 (lowest restraint energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VNMR	6.1C	Varian
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	chemical shift assignment	Sparky		Goddard
5	data analysis	Sparky		Goddard
6	refinement	Amber	14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
7	data analysis	Amber	14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
8	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman