2RO2

Solution structure of domain I of the negative polarity CChMVd hammerhead ribozyme


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
22D 1H-1H TOCSY0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
32D DQF-COSY0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
42D 1H-1H NOESY0.5mM RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA90% H2O/10% D2O12.46ambient281
52D 1H-15N HSQC1mM [U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA90% H2O/10% D2O12.46ambient297
62D HNN COSY1mM [U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA90% H2O/10% D2O12.46ambient297
72D 1H-13C HSQC0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
83D NOESY-HMQC0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
93D HCCH ECOSY0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
102D HCCH-TOCSY0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
113D HCP0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
123D 13C-ED-1H-31P HETCOR0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
133D HCP-CCH TOCSY0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
142D HCNCH0.5mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*GP*AP*CP*CP*UP*GP*AP*AP*GP*UP*GP*GP*GP*UP*UP*UP*CP*CP*C)-3'), 10mM sodium phosphate, 0.1mM EDTA100% D2O12.46ambient297
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
2BrukerAVANCE600
3BrukerAVANCE700
NMR Refinement
MethodDetailsSoftware
simulated annealing and restrained energy minimizationminimized average structure of 29 converged conformers with the least restraint violation energy and total energyTopSpin
NMR Ensemble Information
Conformer Selection CriteriaStructures with the least restraint violations and total energy
Conformers Calculated Total Number100
Conformers Submitted Total Number1
Representative Model1 (minimized average structure)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpin1.3Bruker Biospin
2processingTopSpin1.3Bruker Biospin
3data analysisSparky3.110Goddard
4refinementAmber8.0Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollm