2RPK

Solution Structure of Domain II of the Positive Polarity CCHMVD Hammerhead Ribozyme


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA90% H2O/10% D2O12.46ambient281
22D 1H-1H NOESY0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
32D 1H-1H TOCSY0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
42D 1H-1H COSY0.7 mM RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
52D 1H-15N HSQC0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA90% H2O/10% D2O12.46ambient281
62D 1H-13C HSQC0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
73D 1H,13C HMQC-NOESY0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
83D HCCH-COSY0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
92D HCCH-TOCSY0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
103D HCP0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
113D 13C-ED-1H-31P HETCOR0.4 mM [U-100% 13C; U-100% 15N] RNA (5'-R(*GP*GP*GP*AP*UP*CP*CP*AP*UP*GP*AP*CP*AP*GP*GP*AP*UP*CP*CP*C)-3'), 10 mM sodium phosphate, 0.1 mM EDTA100% D2O12.46ambient296
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
2BrukerAVANCE600
NMR Refinement
MethodDetailsSoftware
simulated annealing and restrained energy minimizationminimized average structure of 33 converged conformers with the least restraint violation energy and total energyTopSpin
NMR Ensemble Information
Conformer Selection Criteriaminimized average structure of 33 converged conformers with the least restraint violation energy and total energy
Conformers Calculated Total Number60
Conformers Submitted Total Number1
Representative Model1 (minimized average structure)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpin1.3Bruker Biospin
2processingTopSpin1.3Bruker Biospin
3chemical shift assignmentSparky3.110Goddard
4data analysisSparky3.110Goddard
5structure solutionAmber8.0Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
6refinementAmber8.0Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm