2L8F | pdb_00002l8f

Structure of a 4X4 Nucleotide RNA Internal Loop from an R2 Retrotransposon

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA	90% H2O/10% D2O	0.1	6.5	ambient	273
2	2D 1H-13C HSQC	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA	90% H2O/10% D2O	0.1	6.5	ambient	273
3	2D 1H-13C HSQC	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA	90% H2O/10% D2O	0.1	5	ambient	273
4	2D 1H-13C HSQC	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10	100% D2O	0.1	6.5	ambient	293
5	2D 1H-1H NOESY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA	90% H2O/10% D2O	0.1	6.5	ambient	273
6	2D 1H-1H NOESY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA	90% H2O/10% D2O	0.1	6.5	ambient	273
7	2D 1H-1H NOESY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA	90% H2O/10% D2O	0.1	6.5	ambient	293
8	2D 1H-1H NOESY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10	100% D2O	0.1	6.5	ambient	293
9	2D 1H-1H NOESY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10	100% D2O	0.1	6.5	ambient	273
10	2D 1H-1H TOCSY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10	100% D2O	0.1	6.5	ambient	293
11	2D 1H-1H TOCSY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10	100% D2O	0.1	6.5	ambient	273
12	2D 1H-1H COSY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10	100% D2O	0.1	6.5	ambient	293
13	2D 31P-1H COSY	1.5 mM RNA (5'-R(*GP*UP*GP*AP*AP*GP*CP*CP*CP*GP*U)-3'), 1.5 mM RNA (5'-R(*CP*GP*GP*AP*GP*GP*AP*CP*AP*CP*U)-3'), 80 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA-10	100% D2O	0.1	6.5	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	500
2	Varian	INOVA	600

NMR Refinement
Method	Details	Software
simulated annealing		NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	no restraint violations; low constraint energy
Conformers Calculated Total Number	40
Conformers Submitted Total Number	10
Representative Model	1 (lowest constraint energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe	2.3	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	chemical shift assignment	Sparky	3.114	Goddard
3	data analysis	Sparky	3.114	Goddard
4	structure solution	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
5	collection	VNMR	6.1C	Varian
6	structure solution	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read
7	refinement	Amber