2KD4

Solution structure and thermodynamics of 2',5' RNA intercalation


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
11H-1H NOESY2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-499.9% D2O2606.51 atm282
231P-1H HETCOR2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-499.9% D2O2606.51 atm282
31H-1H TOCSY2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-499.9% D2O2606.51 atm282
431P-decoupled 1H-1H COSY2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-499.9% D2O2606.51 atm282
51H-1H NOESY with WATERGATE water suppression2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-499.9% D2O1301 atm282
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerDRX600
2BrukerDRX500
NMR Refinement
MethodDetailsSoftware
simulated annealing300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealedxwinnmr
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number10
Conformers Submitted Total Number1
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionxwinnmrBruker Biospin
2data analysisxwinnmrBruker Biospin
3processingxwinnmrBruker Biospin
4chemical shift assignmentSPARKYGoddard
5data analysisSPARKYGoddard
6structure solutionAMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
7refinementAMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm