2JYK
NMR Structure of a 21 bp DNA duplex preferentially cleaved by Human Topoisomerase II
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 90% H2O/10% D2O | 90% H2O/10% D2O | 0.1 | 7.00 | 1 atm | 303 | |
2 | 2D 1H-1H NOESY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
3 | 2D DQF-COSY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
4 | 2D 1H-1H TOCSY | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
5 | 2D 1H-13C HSQC | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 | |
6 | 2D 1H-31P HETCOR | 46mM sodium phosphate; 1mM EDTA; 1.5mM Strand1; 1.5mM Strand2; 100% D2O | 100% D2O | 0.1 | 7.00 | 1 atm | 303 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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Method | Details | Software |
SIMULATED ANNEALING, MOLECULAR DYNAMICS | THE STRUCTURE IS BASED ON A TOTAL OF 670 NOE, 102 HYDROGEN BOND, AND 286 DIHEDRAL RESTRAINTS | X-PLOR NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR NIH | 2.16 | Schwieters, Kuszewski, Tjandra and Clore |
2 | data analysis | MORASS | 2.51 | Luxon |