9QZJ | pdb_00009qzj

SARS-CoV-2 omicron stem-loop-II-motif (s2m_omicron)

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC NH2 only	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	278	Bruker AVANCE III 800
2	BEST-TROSY	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	278	Bruker AVANCE III 800
3	1H-15N CPMG-NOESY	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	278	Bruker AVANCE III 800
4	HNN-COSY	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	278	Bruker AVANCE III 800
5	2D NOESY	50 uM s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	278	Bruker AVANCE III 800
6	3D 1H-13C NOESY	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III HD 700
7	2D 1H-13C HSQC aliphatic	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III HD 700
8	2D 1H-13C HSQC aromatic	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III HD 700
9	BEST-TROSY	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III HD 700
10	CNC	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III 800
11	1H-15N CPMG-NOESY	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III 800
12	2D 1H-1H TOCSY	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III HD 600
13	HCCNH	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III 800
14	3D HCN	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III HD 800
15	2D NOESY	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III HD 800
16	fw-HCCH-TOCSY	680 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	100% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE NEO 600
17	2D NOESY	700 uM [U-13C; U-15N] s2m_omicron, 50 mM potassium chloride, 25 mM potassium phosphate	95% H2O/5% D2O	125 mM	6.2	1 atm	298	Bruker AVANCE III 800

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

NMR Refinement
Method	Details	Software
simulated annealing		ARIA

NMR Ensemble Information
Conformer Selection Criteria	all calculated structures submitted
Conformers Calculated Total Number	20
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	processing	TopSpin		Bruker Biospin
3	chemical shift assignment	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
4	structure calculation	ARIA		Linge, O'Donoghue and Nilges