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An Information Portal to 105097 Biological Macromolecular Structures

SOLUTION NMR
Materials and Methods page
2KF8
  •   NMR Eperiment Details Hide
    Representative Model Choice Rationale
    lowest energy  
     
    Spectrometer Info
    Field Strength 600.0
    Manufacturer Varian
    Model INOVA
    Field Strength 700.0
    Manufacturer Bruker
    Model Avance
    Field Strength 600.0
    Manufacturer Bruker
    Model Avance
     
    Sample Conditions
    IDs solution ID:1 condition ID:1
    Sample Contents 0.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-1, 70mM potassium chloride-2, 20mM potassium phosphate-3, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    pH 7
    Temperature 298
    IDs solution ID:2 condition ID:1
    Sample Contents 0.5-2.5mM DNA (5'-D(*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DT)-3')-4, 70mM potassium chloride-5, 20mM potassium phosphate-6, 100% D2O
    Solvent System 100% D2O
    pH 7
    Temperature 298
     
     
  •   NMR Refinement Information Hide
    Refinement
    Method molecular dynamics
    Details This natural sequence exhibits the same conformation as the 7BRG-substituted sequence, which has a much cleaner NMR spectrum. 10 relaxation matrix intensity-refined structures of the 7BRG form with the lowest energy were taken, the bromine atoms were replaced with hydrogen atoms, and the structures were subsequently subjected to distance-retrained molecular dynamics refinement.
     
  •   NMR Ensemble Information Hide
    Ensemble
    Conformer Selection Criteria all calculated structures submitted
    Conformers Calculated Total Number 10
    Conformers Submitted Total Number 10
     
  •   NMR Experimental Information Hide
    Experiment
    IDs experiment ID:1 solution ID:2 conditons ID:1
    Type 2D 1H-13C HSQC
    IDs experiment ID:2 solution ID:2 conditons ID:1
    Type 2D 1H-1H TOCSY
    IDs experiment ID:3 solution ID:2 conditons ID:1
    Type 2D 1H-1H COSY
    IDs experiment ID:4 solution ID:1 conditons ID:1
    Type 2D 1H-1H NOESY
    IDs experiment ID:5 solution ID:2 conditons ID:1
    Type 2D 1H-1H NOESY
     
  •   Software and Computing Hide
    NMR Software
    Authors Schwieters, Kuszewski, Tjandra, Clore
    Classification refinement
    Software Name X-PLOR_NIH 2.21
    Authors Schwieters, Kuszewski, Tjandra, Clore
    Classification structure solution
    Software Name X-PLOR_NIH 2.21
    Authors Bruker Biospin
    Classification processing
    Software Name TOPSPIN
    Authors Felix NMR, Inc.
    Classification peak picking
    Software Name Felix 2007