9CPI | pdb_00009cpi

Structures of small molecules bound to RNA repeat expansions that cause Huntington's disease-like 2 and myotonic dystrophy type 1

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA	100% D2O	5 mM	6.0	1 atm	308	Bruker AVANCE III HD 700
2	2D DQF-COSY	0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA	100% D2O	5 mM	6.0	1 atm	308	Bruker AVANCE III HD 700
3	2D NOESY	0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA	95% H2O/5% D2O	10 mM	6.0	1 atm	278	Bruker AVANCE III HD 850
4	2D NOESY	0.3 mM RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 0.6 mM 1-(2-ammonioethyl)-2-(4-((4-(4,5-dihydro-1H-imidazol-3-ium-2-yl)phenyl)carbamoyl)phenyl)-4,5-dihydro-1H-imidazol-3-ium, 5 mM potassium phosphate, 0.25 mM EDTA	95% H2O/5% D2O	5 mM	6.0	1 atm	288	Bruker AVANCE III HD 850

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III HD	700
2	Bruker	AVANCE III HD	850

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	TopSpin	3.5	Bruker Biospin
2	structure calculation	Amber		Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
3	chemical shift assignment	NMRFAM-SPARKY	1.3	Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JL
4	peak picking	NMRFAM-SPARKY	1.3	Bioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JL