6FY6
Concerted dynamics of metallo-base pairs in an A/B-form helical transition (major species)
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 | 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION | 100% D2O | 50 mM | 7.35 | ambient atm | 298 | Bruker AVANCE 700 |
6 | 2D 1H-1H NOESY | 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION | 100% D2O | 50 mM | 7.35 | ambient atm | 298 | Bruker AVANCE 600 |
2 | 2D 1H-1H COSY | 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION | 100% D2O | 50 mM | 7.35 | ambient atm | 298 | Bruker AVANCE 600 |
3 | 2D 1H-1H TOCSY | 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION | 100% D2O | 50 mM | 7.35 | ambient atm | 298 | Bruker AVANCE 600 |
7 | 2D 1H-13C HSQC aliphatic | 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION | 100% D2O | 50 mM | 7.35 | ambient atm | 298 | Bruker AVANCE 600 |
8 | 2D 1H-13C HSQC aromatic | 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION | 100% D2O | 50 mM | 7.35 | ambient atm | 298 | Bruker AVANCE 600 |
4 | 2D 1H-1H NOESY | 0.4 mM polydeoxyribonucleotide, 1.2 mM MERCURY (II) ION | 90% H2O/10% D2O | 50 mM | 7.75 | ambient atm | 277 | Bruker AVANCE 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Bruker | AVANCE | 700 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | 2000 preliminary structures were calculated. The 20 lowest energy structures were selected and subsequently refined. Of the 200 refined conformers calculated the 20 lowest energy structures were chosen | Xplor-NIH |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (fewest violations) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 4.0.0.b.16 | Bruker Biospin |
2 | structure calculation | Xplor-NIH | 2.46 | G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra |
3 | chemical shift assignment | Sparky | Goddard | |
4 | peak picking | Sparky | Goddard | |
5 | refinement | Xplor-NIH | 2.46 | G. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandra |