9CPG | pdb_00009cpg

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 4-guanidinophenyl 4-guanidinobenzoate, 5 mM potassium phosphate, 0.25 mM EDTA	100% D2O	5 mM	6.0	1 atm	298	Bruker AVANCE III 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 4-guanidinophenyl 4-guanidinobenzoate, 5 mM potassium phosphate, 0.25 mM EDTA	100% D2O	5 mM	6.0	1 atm	298	Bruker AVANCE III 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 (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol, 5 mM potassium phosphate, 0.25 mM EDTA	95% H2O/5% D2O	5 mM	6.0	1 atm	279	Bruker AVANCE III HD 850

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	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	collection	TopSpin		Bruker Biospin
2	structure calculation	Amber	20	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	data analysis	NMRFAM-SPARKY	1.470	Goddard TD & Kneller DG (2008) SPARKY 3. University of California, San Francisco.