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SOLUTION NMR
Materials and Methods page
2L5Z
  •   NMR Eperiment Details Hide
    Representative Model Choice Rationale
    minimized average  
     
    Spectrometer Info
    Field Strength 800.0
    Manufacturer Varian
    Model INOVA
    Field Strength 600.0
    Manufacturer Varian
    Model INOVA
    Field Strength 500.0
    Manufacturer Varian
    Model INOVA
     
    Sample Conditions
    IDs solution ID:1 condition ID:1
    Sample Contents 0.4-1.8 mM VS ribozyme SVI RNA (26-MER)-1, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:1 condition ID:2
    Sample Contents 0.4-1.8 mM VS ribozyme SVI RNA (26-MER)-1, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:2 condition ID:1
    Sample Contents 0.4-1.8 mM VS ribozyme SVI RNA (26-MER)-2, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:2 condition ID:2
    Sample Contents 0.4-1.8 mM VS ribozyme SVI RNA (26-MER)-2, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:3 condition ID:1
    Sample Contents 0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-3, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:3 condition ID:2
    Sample Contents 0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-3, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:4 condition ID:1
    Sample Contents 0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-4, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:4 condition ID:2
    Sample Contents 0.4-1.8 mM [U-15N] VS ribozyme SVI RNA (26-MER)-4, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:5 condition ID:1
    Sample Contents 0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-5, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:5 condition ID:2
    Sample Contents 0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-5, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:6 condition ID:1
    Sample Contents 0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:6 condition ID:2
    Sample Contents 0.4-1.8 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-6, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:7 condition ID:1
    Sample Contents 0.4 mM [U-15N] VS ribozyme SVI RNA (26-MER)-7, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:7 condition ID:2
    Sample Contents 0.4 mM [U-15N] VS ribozyme SVI RNA (26-MER)-7, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:8 condition ID:1
    Sample Contents 0.4 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-8, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
    IDs solution ID:8 condition ID:2
    Sample Contents 0.4 mM [U-13C; U-15N] VS ribozyme SVI RNA (26-MER)-8, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 50 mM KCl and 5 mM MgCl2
    pH 6.5
    Pressure ambient
    Pressure Units atm
    Temperature 288
     
     
  •   NMR Refinement Information Hide
    Refinement
    Method simulated annealing, molecular dynamics
     
  •   NMR Ensemble Information Hide
    Ensemble
    Conformer Selection Criteria structures with the lowest energy
    Conformers Calculated Total Number 500
    Conformers Submitted Total Number 21
     
  •   NMR Experimental Information Hide
    Experiment
    IDs experiment ID:1 solution ID:6 conditons ID:2
    Type 2D 1H-13C CT-HSQC
    IDs experiment ID:10 solution ID:5 conditons ID:1
    Type 2D H(NCCC)H for uracil and cytosine residues
    IDs experiment ID:11 solution ID:5 conditons ID:1
    Type 2D H(NC)-TOCSY-(C)H for guanosine residues
    IDs experiment ID:12 solution ID:5 conditons ID:1
    Type 2D (H)N(C)-TOCSY-(C)H for adenosine residues
    IDs experiment ID:13 solution ID:3 conditons ID:1
    Type 2D 1H-15N CPMG-NOESY
    IDs experiment ID:14 solution ID:4 conditons ID:2
    Type 2D 1H 15N HMQC optimized for transfers via J=7.0 Hz and J=21 Hz
    IDs experiment ID:15 solution ID:3 conditons ID:1
    Type 2D HNN-COSY
    IDs experiment ID:16 solution ID:2 conditons ID:2
    Type 2D DQF COSY
    IDs experiment ID:17 solution ID:6 conditons ID:2
    Type 3D HCCH-E.COSY
    IDs experiment ID:18 solution ID:7 conditons ID:1
    Type 2D imino-optimized 2D 1H-15N HSQC
    IDs experiment ID:19 solution ID:8 conditons ID:2
    Type Spin-state selective experiments
    IDs experiment ID:2 solution ID:6 conditons ID:2
    Type 2D 1H-13C HMQC
    IDs experiment ID:20 solution ID:6 conditons ID:2
    Type Spin-state selective experiments
    IDs experiment ID:3 solution ID:6 conditons ID:2
    Type 2D 1H-15N MQ-(HC)N(C)H
    IDs experiment ID:4 solution ID:6 conditons ID:2
    Type 3D CT-HCCH-COSY
    IDs experiment ID:5 solution ID:6 conditons ID:2
    Type 3D HCCH-TOCSY
    IDs experiment ID:6 solution ID:6 conditons ID:2
    Type 3D 13C-edited HMQC-NOESY
    IDs experiment ID:7 solution ID:1 conditons ID:1
    Type 1D flip-back watergate 1H
    IDs experiment ID:8 solution ID:1 conditons ID:1
    Type 2D flip-back watergate NOESY
    IDs experiment ID:9 solution ID:3 conditons ID:1
    Type 2D imino- and amino-optimized 2D 1H-15N HSQC
     
  •   Software and Computing Hide
    NMR Software
    Authors PyMol (Schr dinger)
    Classification structure analysis
    Software Name PyMol
    Authors PyMol (Schr dinger)
    Classification structure display
    Software Name PyMol
    Authors (CURVES) Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K.
    Classification structure analysis
    Software Name CURVES_+
    Authors Schwieters, Kuszewski, Tjandra and Clore
    Classification refinement
    Software Name X-PLOR_NIH
    Authors Schwieters, Kuszewski, Tjandra and Clore
    Classification structure solution
    Software Name X-PLOR_NIH
    Authors Johnson, One Moon Scientific
    Classification peak picking
    Software Name NMRView
    Authors Johnson, One Moon Scientific
    Classification chemical shift assignment
    Software Name NMRView
    Authors Johnson, One Moon Scientific
    Classification data analysis
    Software Name NMRView
    Authors Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
    Classification data analysis
    Software Name NMRDraw
    Authors (Module)
    Classification data analysis
    Software Name Module 1.0