9SYC | pdb_00009syc

Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GAAG reweighted MD subensemble

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	1.3 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 600
2	2D 1H-13C HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE NEO 900
3	2D 1H-13C HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 20 mg/mL Pf1 phage	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE NEO 900
4	2D 1H-15N HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE NEO 900
5	2D 1H-15N HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 20 mg/mL Pf1 phage	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE NEO 900
6	3D qHCP	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 700
7	2D qHCP	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 700
8	2D P-FIDS	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 600
9	3D HCC-TOCSY-CCH-E.COSY	1.24 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	95% H2O/5% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE 600
10	2D HNN-COSY	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 600
11	2D gamma HCCH	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 700
12	2D gamma HCNCH	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 700
13	2D gamma HCP	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE 600
14	2D 1H-13C HSQC	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 600
15	2D 1H-15N HSQC	1.24 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	95% H2O/5% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 600
16	2D HCN	1.24 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	95% H2O/5% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE 600
17	3D forward directed HCCH-TOCSY	0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE 600
18	2D 1H-1H NOESY	1.26 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS	95% H2O/5% D2O	50 mM	6.4	1 atm	298	Bruker AVANCE III HD 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE III HD	600
3	Bruker	AVANCE III HD	700
5	Bruker	AVANCE NEO	900

NMR Refinement
Method	Details	Software
molecular dynamics	initial MD simulation was reweighted with the BME approach (https://github.com/KULL-Centre/BME), with NOE RDC, J-coupling and CCR data	GROMACS

NMR Ensemble Information
Conformer Selection Criteria	back calculated data agree with NOE, RDC, J-coupling and CCR data
Conformers Calculated Total Number	20100
Conformers Submitted Total Number	100
Representative Model	1 (first conformer of largest cluster)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	TopSpin		Bruker Biospin
2	collection	TopSpin		Bruker Biospin
3	peak picking	NMRFAM-SPARKY	1.470	Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
4	chemical shift assignment	NMRFAM-SPARKY	1.470	Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
5	data analysis	PALES		Zweckstetter and Bax
8	structure calculation	GROMACS		https://www.gromacs.org/