2N2P | pdb_00002n2p

Solution structure of a double base-pair inversion mutant of murine tumour necrosis factor alpha CDE-23 RNA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
2	2D 1H-13C HSQC	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
3	immino-1H-1H NOESY	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	90% H2O/10% D2O	20	6.5	ambient	300
4	3D-HCCH-COSY-TOCSY	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
5	3D HsCNb/HbCNb	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
6	2D HNN-COSY	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	90% H2O/10% D2O	20	6.5	ambient	300
7	3D 13C-edited NOESY	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
8	2D COSY	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
9	1H-31P HET-COR(P,H-COSY-H,C-HMQC)	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
10	T1-13C-EDIT relaxation	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
11	T1rho-13C-EDIT relaxation	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate	100% D2O	20	6.5	ambient	300
12	13C-base edited IPAP	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate, 30 mg/mL Pf1 phage	100% D2O	20	6.5	ambient	300
13	13C-sugar edited IPAP	0.35 mM [U-100% 13C; U-100% 15N] RNA, 20 mM sodium phosphate, 30 mg/mL Pf1 phage	100% D2O	20	6.5	ambient	300

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	700
2	Bruker	AVANCE	600
3	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
DGSA-distance geometry simulated annealing		ARIA

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	ARIA	1.2	Linge, O'Donoghue and Nilges
2	chemical shift assignment	CCPN_Analysis	2.3	CCPN
3	collection	TopSpin	3.0	Bruker Biospin
4	structure solution	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read
5	refinement	CNS	1.1	Brunger, Adams, Clore, Gros, Nilges and Read

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.