1FQZ

NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6	90% H2O/10% D2O	8mM Na phosphate	6.6	ambient	278
2	2D NOESY	1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6	100% D2O	8mM Na phosphate	6.6	ambient	278
3	2D NOESY	1.2 mM RNA, 8mM sodium phosphate buffer pH 6.6	100% D2O	8mM Na phosphate	6.6	ambient	298
4	2D NOESY	8mM Na phosphate	6.6	ambient	298

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

NMR Refinement
Method	Details	Software
Using a motif-based approach, a model was constructed from X-ray and NMR structures of 6 known RNA motifs: (i) double helix, (ii) sheared G.A base pair, (iii) eukaryotic loop E motif, (iv) S-turn, (v) trans Wobble G.U pair, (vi) U-turn. The resulting energy minimized model was then validated by comparing it with the NOESY data.	Motifs (i) to (vi) were obtained from the following sources: (i) idealized A-form coordinates (InsightII, MSI); (ii)&(iii) PDB 430D.pdb; (iv) PDB 1ETG.pdb; (vi) PDB 1QA6.pdb; Motif (v) was constructed manually.	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with acceptable covalent geometry, structures with favorable non-bond energy
Conformers Calculated Total Number	1
Conformers Submitted Total Number	1

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.5	Bruker
2	processing	NMRPipe	1.7	Delaglio
3	data analysis	Sparky	3.66	Goddard & Kneller
4	refinement	CHARMM	25.2	Brooks et al.
5	refinement	Insight II	97.0	MSI