9SY8 | pdb_00009sy8

Beyond single-state RNA structural biology: MD/NMR description of temperature-sensitive dynamic RNA ensembles - GAAG ARIA structure


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY1.3 mM RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE III HD 600
22D 1H-13C HSQC0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE NEO 900
32D 1H-13C HSQC0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 20 mg/mL Pf1 phage100% D2O50 mM6.41 atm298Bruker AVANCE NEO 900
42D 1H-15N HSQC0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE NEO 900
52D 1H-15N HSQC0.2 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS, 20 mg/mL Pf1 phage100% D2O50 mM6.41 atm298Bruker AVANCE NEO 900
63D qHCP0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE III HD 700
72D qHCP0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE III HD 700
82D P-FIDS0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE III HD 600
93D HCC-TOCSY-CCH-E.COSY0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE 600
102D HNN-COSY1.24 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS95% H2O/5% D2O50 mM6.41 atm298Bruker AVANCE III HD 600
112D gamma HCCH0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE III HD 700
122D gamma HCNCH0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE III HD 700
132D gamma HCP0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE 600
142D 1H-13C HSQC0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE III HD 600
152D 1H-15N HSQC1.24 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS95% H2O/5% D2O50 mM6.41 atm298Bruker AVANCE III HD 600
162D HCN1.24 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS95% H2O/5% D2O50 mM6.41 atm298Bruker AVANCE 600
173D forward directed HCCH-TOCSY0.64 mM [U-13C; U-15N] RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS100% D2O50 mM6.41 atm298Bruker AVANCE 600
192D 1H-1H NOESY1.26 mM RNA hairpin with GAAG tetraloop, 50 mM potassium phosphate, 50 uM DSS95% H2O/5% D2O50 mM6.41 atm298Bruker AVANCE III HD 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
6BrukerAVANCE III HD600
2BrukerAVANCE III HD700
3BrukerAVANCE III800
4BrukerAVANCE NEO900
5BrukerAVANCE III950
NMR Refinement
MethodDetailsSoftware
simulated annealingCNS
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number200
Conformers Submitted Total Number20
Representative Model1 (closest to the average)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingTopSpin4.2.0Bruker Biospin
2collectionTopSpin4.20Bruker Biospin
3peak pickingNMRFAM-SPARKY1.470Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
4chemical shift assignmentNMRFAM-SPARKY1.470Lee W, Tonelli M, Markley JL Goddard TD, and Kneller DG
5data analysisPALESZweckstetter and Bax
6structure calculationCNSBrunger, Adams, Clore, Gros, Nilges and Read
7structure calculationARIALinge, O'Donoghue and Nilges