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SOLUTION NMR
Materials and Methods page
2MB3
  •   NMR Eperiment Details Hide
    Representative Model Choice Rationale
    lowest energy  
     
    Spectrometer Info
    Field Strength 400.0
    Manufacturer Bruker
    Model AMX
    Field Strength 700.0
    Manufacturer Bruker
    Model AMX
    Field Strength 600.0
    Manufacturer Bruker
    Model AMX
     
    Sample Conditions
    IDs solution ID:1 condition ID:1
    Sample Contents 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 90
    pH 7
    Pressure ambient
    Pressure Units atm
    Temperature 310
    IDs solution ID:1 condition ID:2
    Sample Contents 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 90
    pH 7
    Temperature 298
    IDs solution ID:1 condition ID:3
    Sample Contents 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 40
    pH 7
    Temperature 298
    IDs solution ID:2 condition ID:1
    Sample Contents 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 90
    pH 7
    Pressure ambient
    Pressure Units atm
    Temperature 310
    IDs solution ID:2 condition ID:2
    Sample Contents 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 90
    pH 7
    Temperature 298
    IDs solution ID:2 condition ID:3
    Sample Contents 0.2-2 mM DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-2 mM L2H, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 40
    pH 7
    Temperature 298
    IDs solution ID:3 condition ID:1
    Sample Contents 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 90
    pH 7
    Pressure ambient
    Pressure Units atm
    Temperature 310
    IDs solution ID:3 condition ID:2
    Sample Contents 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 90
    pH 7
    Temperature 298
    IDs solution ID:3 condition ID:3
    Sample Contents 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 40
    pH 7
    Temperature 298
    IDs solution ID:4 condition ID:1
    Sample Contents 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 90
    pH 7
    Pressure ambient
    Pressure Units atm
    Temperature 310
    IDs solution ID:4 condition ID:2
    Sample Contents 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 90
    pH 7
    Temperature 298
    IDs solution ID:4 condition ID:3
    Sample Contents 0.2 mM [U-99% 13C; U-99% 15N] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2 mM L2H, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 40
    pH 7
    Temperature 298
    IDs solution ID:5 condition ID:1
    Sample Contents 0.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 90
    pH 7
    Pressure ambient
    Pressure Units atm
    Temperature 310
    IDs solution ID:5 condition ID:2
    Sample Contents 0.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 90
    pH 7
    Temperature 298
    IDs solution ID:5 condition ID:3
    Sample Contents 0.2-1 mM [U-4% 13C] DNA (5'-D(*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*A)-3'), 0.2-1 mM L2H, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 40
    pH 7
    Temperature 298
     
     
  •   NMR Refinement Information Hide
    Refinement
    Method DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics
     
  •   NMR Ensemble Information Hide
    Ensemble
    Conformer Selection Criteria structures with the lowest energy
    Conformers Calculated Total Number 100
    Conformers Submitted Total Number 10
     
  •   NMR Experimental Information Hide
    Experiment
    IDs experiment ID:1 solution ID:2 conditons ID:3
    Type 2D 1H-1H TOCSY
    IDs experiment ID:10 solution ID:5 conditons ID:2
    Type 2D 1H-13C HSQC aliphatic
    IDs experiment ID:11 solution ID:4 conditons ID:2
    Type 2D 1H-13C HSQC aliphatic
    IDs experiment ID:12 solution ID:4 conditons ID:2
    Type 2D 1H-13C HSQC aromatic
    IDs experiment ID:13 solution ID:3 conditons ID:2
    Type 1D JRHMBC
    IDs experiment ID:14 solution ID:2 conditons ID:3
    Type 2D 1H-31P HSQC
    IDs experiment ID:2 solution ID:1 conditons ID:3
    Type 2D 1H-1H TOCSY
    IDs experiment ID:3 solution ID:1 conditons ID:3
    Type 2D 1H-1H NOESY
    IDs experiment ID:4 solution ID:2 conditons ID:3
    Type 2D 1H-1H NOESY
    IDs experiment ID:5 solution ID:2 conditons ID:1
    Type 2D 1H-1H NOESY
    IDs experiment ID:6 solution ID:2 conditons ID:2
    Type 2D 1H-1H NOESY
    IDs experiment ID:7 solution ID:2 conditons ID:3
    Type 2D 1H-13C HSQC aromatic
    IDs experiment ID:8 solution ID:5 conditons ID:2
    Type 2D 1H-13C HSQC aromatic
    IDs experiment ID:9 solution ID:2 conditons ID:3
    Type 2D 1H-13C HSQC aliphatic
     
  •   Software and Computing Hide
    NMR Software
    Authors Bruker Biospin
    Classification collection
    Software Name TOPSPIN
    Authors Schwieters, Kuszewski, Tjandra and Clore
    Classification structure solution
    Software Name X-PLOR_NIH
    Authors Schwieters, Kuszewski, Tjandra and Clore
    Classification refinement
    Software Name X-PLOR_NIH
    Authors Goddard
    Classification peak picking
    Software Name SPARKY
    Authors Goddard
    Classification chemical shift assignment
    Software Name SPARKY
    Authors Goddard
    Classification data analysis
    Software Name SPARKY
    Authors Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo and Kollman
    Classification refinement
    Software Name AMBER