Experiment: 9SYF

Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GCAA MD conformational ensemble

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.7 mM RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE NEO 900
2	2D 1H-13C HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	90% H2O/10% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III 800
3	2D 1H-13C HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS, 20 mg/mL Pf1 phage	90% H2O/10% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III 800
4	2D 1H-15N HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	90% H2O/10% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III 800
5	2D 1H-15N HSQC	0.2 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS, 20 mg/mL Pf1 phage	90% H2O/10% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III 800
6	3D qHCP	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
7	2D qHCP	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
8	2D P-FIDS	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
9	3D HCC-TOCSY-CCH-E.COSY	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE 600
10	2D HNN-COSY	0.7 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	90% H2O/10% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 600
11	2D gamma HCCH	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
12	2D gamma HCNCH	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
13	2D gamma HCP	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 700
14	2D 1H-13C HSQC	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE NEO 900
15	2D 1H-15N HSQC	0.7 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	90% H2O/10% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE 600
16	2D HCN	0.7 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	90% H2O/10% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE 600
17	3D forward directed HCCH-TOCSY	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 600
18	3D HCP	0.5 mM [U-13C; U-15N] RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	100% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III HD 600
19	2D 1H-1H NOESY	0.6 mM RNA hairpin with GCAA tetraloop, 50 mM potassium phosphate, 50 uM DSS	95% H2O/5% D2O	50 mM	6.4	1 atm	308	Bruker AVANCE III 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE III HD	600
3	Bruker	AVANCE III HD	700
4	Bruker	AVANCE III	800
5	Bruker	AVANCE NEO	900

NMR Refinement
Method	Details	Software
molecular dynamics	initial MD frames were reweighted with the BME approach using back calculated NOE; RDC, J-couplings and CCR	GROMACS

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	TopSpin	4.2.0	Bruker Biospin
2	collection	TopSpin	4.2.0	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
6	structure calculation	GROMACS		https://www.gromacs.org/

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

9SYF | pdb_00009syf

Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GCAA MD conformational ensemble