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An Information Portal to 105097 Biological Macromolecular Structures

SOLUTION NMR
Materials and Methods page
2M23
  •   NMR Eperiment Details Hide
    Representative Model Choice Rationale
    lowest energy  
     
    Spectrometer Info
    Field Strength 500.0
    Manufacturer Bruker
    Model Avance
    Field Strength 600.0
    Manufacturer Bruker
    Model Avance
    Field Strength 700.0
    Manufacturer Bruker
    Model Avance
     
    Sample Conditions
    IDs solution ID:1 condition ID:1
    Sample Contents 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 298
    IDs solution ID:1 condition ID:2
    Sample Contents 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 278
    IDs solution ID:1 condition ID:3
    Sample Contents 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 293
    IDs solution ID:2 condition ID:1
    Sample Contents 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 298
    IDs solution ID:2 condition ID:2
    Sample Contents 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 278
    IDs solution ID:2 condition ID:3
    Sample Contents 0.5-0.9 mM RNA (29-MER), 0.5-0.9 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 293
    IDs solution ID:3 condition ID:1
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 298
    IDs solution ID:3 condition ID:2
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 278
    IDs solution ID:3 condition ID:3
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 293
    IDs solution ID:4 condition ID:1
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 298
    IDs solution ID:4 condition ID:2
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 278
    IDs solution ID:4 condition ID:3
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 293
    IDs solution ID:5 condition ID:1
    Sample Contents 0.6 mM [3',4',5',5'',5-100% 2H] RNA (29-MER), 0.6 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 298
    IDs solution ID:5 condition ID:2
    Sample Contents 0.6 mM [3',4',5',5'',5-100% 2H] RNA (29-MER), 0.6 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 278
    IDs solution ID:5 condition ID:3
    Sample Contents 0.6 mM [3',4',5',5'',5-100% 2H] RNA (29-MER), 0.6 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 100% D2O
    Solvent System 100% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 293
    IDs solution ID:6 condition ID:1
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 298
    IDs solution ID:6 condition ID:2
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 278
    IDs solution ID:6 condition ID:3
    Sample Contents 0.5 mM [U-100% 13C; U-100% 15N] RNA (29-MER), 0.5 mM RNA (5'-R(*CP*AP*GP*UP*GP*UP*C)-3'), 110 mM potassium chloride, 10 uM EDTA, 25.6 mg/mL Pf1 phage, 90% H2O/10% D2O
    Solvent System 90% H2O/10% D2O
    Ionic Strength 110
    pH 6.8
    Pressure ambient
    Temperature 293
     
     
  •   NMR Refinement Information Hide
    Refinement
    Method molecular dynamics, torsion angle dynamics
     
  •   NMR Ensemble Information Hide
    Ensemble
    Conformer Selection Criteria structures with the lowest energy
    Conformers Calculated Total Number 200
    Conformers Submitted Total Number 20
     
  •   NMR Experimental Information Hide
    Experiment
    IDs experiment ID:1 solution ID:1 conditons ID:1
    Type 2D 1H-1H NOESY
    IDs experiment ID:10 solution ID:3 conditons ID:1
    Type 2D 1H-13C HSQC aliphatic
    IDs experiment ID:11 solution ID:3 conditons ID:1
    Type 2D 1H-13C HSQC aromatic
    IDs experiment ID:12 solution ID:2 conditons ID:2
    Type 2D 1H-1H NOESY
    IDs experiment ID:13 solution ID:2 conditons ID:2
    Type 2D 1H-1H NOESY
    IDs experiment ID:14 solution ID:2 conditons ID:3
    Type 2D 1H-1H NOESY
    IDs experiment ID:15 solution ID:4 conditons ID:2
    Type 2D JNN HNN COSY
    IDs experiment ID:16 solution ID:1 conditons ID:1
    Type 1D-31P
    IDs experiment ID:17 solution ID:4 conditons ID:1
    Type F1,2 X-filtered 1H-1H NOESY
    IDs experiment ID:18 solution ID:4 conditons ID:1
    Type F1,2 X-filtered 1H-1H TOCSY
    IDs experiment ID:2 solution ID:1 conditons ID:1
    Type 2D 1H-1H NOESY
    IDs experiment ID:3 solution ID:1 conditons ID:1
    Type 2D 1H-1H TOCSY
    IDs experiment ID:4 solution ID:5 conditons ID:1
    Type 2D 1H-1H NOESY
    IDs experiment ID:5 solution ID:4 conditons ID:1
    Type 2D 1H-13C HSQC aliphatic
    IDs experiment ID:6 solution ID:6 conditons ID:1
    Type 2D 1H-13C HSQC aliphatic
    IDs experiment ID:7 solution ID:4 conditons ID:2
    Type 2D 1H-15N HSQC
    IDs experiment ID:8 solution ID:4 conditons ID:1
    Type 2D 1H-13C HSQC aromatic
    IDs experiment ID:9 solution ID:6 conditons ID:1
    Type 2D 1H-13C HSQC aromatic
     
  •   Software and Computing Hide
    NMR Software
    Authors Schwieters, Kuszewski, Tjandra and Clore
    Classification refinement
    Software Name X-PLOR_NIH 2.24
    Authors Schwieters, Kuszewski, Tjandra and Clore
    Classification structure solution
    Software Name X-PLOR_NIH 2.24
    Authors Brunger, Adams, Clore, Gros, Nilges and Read
    Classification structure solution
    Software Name CNSSOLVE 1.2
    Authors Guntert, Braun and Wuthrich
    Classification data analysis
    Software Name DYANA 1.5
    Authors Bruker Biospin
    Classification processing
    Software Name TOPSPIN 1.3, 2.0, 2.1
    Authors Bruker Biospin
    Classification collection
    Software Name TOPSPIN 1.3, 2.0, 2.1
    Authors Goddard
    Classification peak picking
    Software Name SPARKY 3.1
    Authors Goddard
    Classification data analysis
    Software Name SPARKY 3.1
    Authors Goddard
    Classification chemical shift assignment
    Software Name SPARKY 3.1