1G1N
NICKED DECAMER DNA WITH PEG6 TETHER, NMR, 30 STRUCTURES
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.5 mM DNA; Phosphate buffer (38 mM NaCl, 38 mM K3PO4) | 90% H2O/10% D2O | 152 mM of monovalent cations | 7.0 | ambient | 283 | |
2 | 2D NOESY | 1.5 mM DNA; Phosphate buffer (38 mM NaCl, 38 mM K3PO4) | 100% D2O | 152 mM of monovalent cations | 7.0 | ambient | 300 | |
3 | E-COSY | 1.5 mM DNA; Phosphate buffer (38 mM NaCl, 38 mM K3PO4) | 100% D2O | 152 mM of monovalent cations | 7.0 | ambient | 300 | |
4 | HSQC | 1.5 mM DNA; Phosphate buffer (38 mM NaCl, 38 mM K3PO4) | 100% D2O | 152 mM of monovalent cations | 7.0 | ambient | 300 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 500 |
NMR Refinement | ||
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Method | Details | Software |
Simulated Annealing, Restrained Molecular Dynamics, Iterative Relaxation Matrix Analysis | The structures are based on a total of 514 restraints, 285 are NOE-derived distance constraints, 175 dihedral angle restraints, 54 distance restraints from hydrogen bonds. The NOE-derived distance constraints were derived from 2D-NOESY spectra (mix. times 50, 75, 100 and 150 ms), using the Iterative Relaxation Matrix Analysis procedure. The final structures were derived by averaging coordinates of 100 structures obtained from IRMA cycles and subsequent 350 ps trajectory of restrained molecular dynamics and energy minimisation. R factor value: 0.41 +/- 0.01; R(1/6) value: 0.0045 +/- 0.0001; RMSD value: 1.22 +/- 0.51; The R and R(1/6) - factors are defined: R = SUM{|I(OBS) - I(CALC)|} / SUM{|I(OBS)|} R(1/6)=SQR(SUM{|I(OBS)^(1/6) - I(CALC)^(1/6)|}^2) / SUM{I(OBS)^(1/6)} Where I(OBS) and I(CALC) are the observed and the calculated NOE intensites. | Discover |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 350 |
Conformers Submitted Total Number | 30 |
Representative Model | 6 (n/a) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear and heteronuclear techniques |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Discover | 98.0 | MSI INSIGHT II package |
2 | iterative matrix relaxation | IRMA | 98.0 | MSI INSIGHT II package |
3 | processing | Felix | 98.0 | MSI INSIGHT II package |
4 | processing | VNMR | 6.1B | Varian |