2HPX
13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
2 | 2D TOCSY | 2.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
3 | E-COSY | 2.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
4 | PH-COSY | 2.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
5 | HP-HSQC | 2.0 mM duplex DNA containing a 4'-oxidized abasic site, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
6 | 2D NOESY | 2.0 mM duplex DNA containing a 4'-oxidized abasic site, 0.2 mM EDTA | 90%D2O/10% H2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 277 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Home-built | Custom-built | 750 |
2 | Home-built | Custom-built | 591 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing matrix relaxation | the structures are based on 410 NOE-derived distance constraints, 43 dihedral angle restraints,8 distance restraints from hydrogen bonds. | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 30 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | The structure model was determined using standard 2D homonuclear and heteronuclear techniques |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 8.0 | Case, D.A. et al. |
2 | data analysis | Felix | 2000 | |
3 | data analysis | MARDIGRAS |