2MTK

NMR structure of the III-IV-V three-way junction from the VS ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	1D flip-back watergate 1H	1.5-2.0 mM [U-100% 15N] J345	90% H2O/10% D2O	55	6.5		288
2	2D 1H-15N HSQC	1.5-2.0 mM [U-100% 15N] J345	90% H2O/10% D2O	55	6.5		288
3	2D 1H-15N HSQC NH2 only	1.5-2.0 mM [U-100% 15N] J345	90% H2O/10% D2O	55	6.5		288
4	3D 1H-15N NOESY	1.5-2.0 mM [U-100% 15N] J345	90% H2O/10% D2O	55	6.5		288
5	2D 1H-13C HSQC	2.0 mM [U-100% 13C; U-100% 15N] J345	100% D2O	55	6.5		298
6	3D 13C-edited HMQC-NOESY	2.0 mM [U-100% 13C; U-100% 15N] J345	100% D2O	55	6.5		298
7	3D CT-HCCH-COSY	2.0 mM [U-100% 13C; U-100% 15N] J345	100% D2O	55	6.5		298
8	3D HCCH-TOCSY	2.0 mM [U-100% 13C; U-100% 15N] J345	100% D2O	55	6.5		298
9	3D 15N-edited NOESY-HSQC	2.0 mM [U-100% 13C; U-100% 15N] J345	90% H2O/10% D2O	55	6.5		298
10	2D H(NC)-TOCSY-(C)H for guanosine residues	2.0 mM [U-100% 13C; U-100% 15N] J345	90% H2O/10% D2O	55	6.5		298
11	2D 1H-13C HMQC	2.0 mM [U-100% 13C; U-100% 15N] J345	100% D2O	55	6.5		298
12	2D 1H-15N MQ-(HC)N(C)H	2.0 mM [U-100% 13C; U-100% 15N] J345	100% D2O	55	6.5		298
13	2D 1H-15N CPMG-NOESY	1.5-2.0 mM [U-100% 15N] J345	90% H2O/10% D2O	55	6.5		288
14	2D HNN-COSY	1.5-2.0 mM [U-100% 15N] J345	90% H2O/10% D2O	55	6.5		288

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	UNITY	600

NMR Refinement
Method	Details	Software
simulated annealing		NMRDraw

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	300
Conformers Submitted Total Number	21
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
2	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	data analysis	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
4	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	chemical shift assignment	CCPNMR_suite		CCPN
6	data analysis	CCPNMR_suite		CCPN
7	peak picking	CCPNMR_suite		CCPN
8	structure solution	X-PLOR_NIH		Schwieters, Kuszewski, Tjandra and Clore
9	refinement	X-PLOR_NIH		Schwieters, Kuszewski, Tjandra and Clore

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.