2KTZ | pdb_00002ktz

Inhibitor Induced Structural Change in the HCV IRES Domain IIa RNA

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	400 uM RNA (38-MER)-1, 150 mM sodium chloride-2, 150 mM potassium chloride-3, 10 mM sodium phosphate-4, 2 mM spermine-5, 2.8 mM ISH-6	100% D2O	0.150 NaCl	7	ambient	308
2	2D 1H-15N HSQC	.4 mM [U-100% 13C; U-100% 15N] RNA (38-MER)-13, 150 mM sodium chloride-14, 150 mM potassium chloride-15, 10 mM sodium phosphate-16, 2 mM spermine-17, 2.8 mM ISH-18	90% H2O/10% D2O	0.150 NaCl	7	ambient	283
3	2D 1H-13C HSQC	.4 mM [U-100% 13C; U-100% 15N] RNA (38-MER)-7, 150 mM sodium chloride-8, 150 mM potassium chloride-9, 10 mM sodium phosphate-10, 2 mM spermine-11, 2.8 mM ISH-12	100% D2O	0.150 NaCl	7	ambient	308
4	2D 1H-1H TOCSY	400 uM RNA (38-MER)-1, 150 mM sodium chloride-2, 150 mM potassium chloride-3, 10 mM sodium phosphate-4, 2 mM spermine-5, 2.8 mM ISH-6	100% D2O	0.150 NaCl	7	ambient	308
5	2D HCCH COSY	.4 mM [U-13C; U-15N]-Ura, Ade RNA (38-MER)-19, 150 mM sodium chloride-20, 150 mM potassium chloride-21, 10 mM sodium phosphate-22, 2 mM spermine-23, 2.8 mM ISH-24	100% D2O	0.150 NaCl	7	ambient	308
6	2D 1H-1H F1fF2f-NOESY	.4 mM [U-13C; U-15N]-Ura, Ade RNA (38-MER)-19, 150 mM sodium chloride-20, 150 mM potassium chloride-21, 10 mM sodium phosphate-22, 2 mM spermine-23, 2.8 mM ISH-24	100% D2O	0.150 NaCl	7	ambient	308
7	2D 1H-1H F1fF2e-NOESY	.4 mM [U-13C; U-15N]-Ura, Ade RNA (38-MER)-19, 150 mM sodium chloride-20, 150 mM potassium chloride-21, 10 mM sodium phosphate-22, 2 mM spermine-23, 2.8 mM ISH-24	100% D2O	0.150 NaCl	7	ambient	308
8	2D 1H-13C HSQC-IPAP	.4 mM [U-13C; U-15N]-Ura, Ade RNA (38-MER)-19, 150 mM sodium chloride-20, 150 mM potassium chloride-21, 10 mM sodium phosphate-22, 2 mM spermine-23, 2.8 mM ISH-24	100% D2O	0.150 NaCl	7	ambient	304
9	2D HCCH COSY-IPAP	.4 mM [U-13C; U-15N]-Ura, Ade RNA (38-MER)-19, 150 mM sodium chloride-20, 150 mM potassium chloride-21, 10 mM sodium phosphate-22, 2 mM spermine-23, 2.8 mM ISH-24	100% D2O	0.150 NaCl	7	ambient	304
10	2D 1H-1H F1fF2f-NOESY	.4 mM [U-13C; U-15N]-Gua, Cyt RNA (38-MER)-25, 150 mM sodium chloride-26, 150 mM potassium chloride-27, 10 mM sodium phosphate-28, 2 mM spermine-29, 2.8 mM ISH-30	100% D2O	0.150 NaCl	7	ambient	308
11	2D 1H-1H F1fF2e-NOESY	.4 mM [U-13C; U-15N]-Gua, Cyt RNA (38-MER)-25, 150 mM sodium chloride-26, 150 mM potassium chloride-27, 10 mM sodium phosphate-28, 2 mM spermine-29, 2.8 mM ISH-30	100% D2O	0.150 NaCl	7	ambient	308
12	2D 1H-13C HSQC	.4 mM [U-13C; U-15N]-Ura, Ade RNA (38-MER)-19, 150 mM sodium chloride-20, 150 mM potassium chloride-21, 10 mM sodium phosphate-22, 2 mM spermine-23, 2.8 mM ISH-24	100% D2O	0.150 NaCl	7	ambient	308
13	2D 1H-13C HSQC	.4 mM [U-13C; U-15N]-Gua, Cyt RNA (38-MER)-25, 150 mM sodium chloride-26, 150 mM potassium chloride-27, 10 mM sodium phosphate-28, 2 mM spermine-29, 2.8 mM ISH-30	100% D2O	0.150 NaCl	7	ambient	308
14	2D 1H-13C HSQC-IPAP	.4 mM [U-13C; U-15N]-Gua, Cyt RNA (38-MER)-25, 150 mM sodium chloride-26, 150 mM potassium chloride-27, 10 mM sodium phosphate-28, 2 mM spermine-29, 2.8 mM ISH-30	100% D2O	0.150 NaCl	7	ambient	304
15	2D HCCH COSY-IPAP	.4 mM [U-13C; U-15N]-Gua, Cyt RNA (38-MER)-25, 150 mM sodium chloride-26, 150 mM potassium chloride-27, 10 mM sodium phosphate-28, 2 mM spermine-29, 2.8 mM ISH-30	100% D2O	0.150 NaCl	7	ambient	304
16	2D HCCH COSY	.4 mM [U-13C; U-15N]-Gua, Cyt RNA (38-MER)-25, 150 mM sodium chloride-26, 150 mM potassium chloride-27, 10 mM sodium phosphate-28, 2 mM spermine-29, 2.8 mM ISH-30	100% D2O	0.150 NaCl	7	ambient	308
17	2D 1H-1H F1fF2e-NOESY	.4 mM [U-100% 13C; U-100% 15N] RNA (38-MER)-7, 150 mM sodium chloride-8, 150 mM potassium chloride-9, 10 mM sodium phosphate-10, 2 mM spermine-11, 2.8 mM ISH-12	100% D2O	0.150 NaCl	7	ambient	308
18	2D 1H-15N HSQC	.4 mM [U-100% 13C; U-100% 15N] RNA (38-MER)-13, 150 mM sodium chloride-14, 150 mM potassium chloride-15, 10 mM sodium phosphate-16, 2 mM spermine-17, 2.8 mM ISH-18	90% H2O/10% D2O	0.150 NaCl	7	ambient	283

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

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	16
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	10	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm