5MVB
Solution structure of a human G-Quadruplex hybrid-2 form in complex with a Gold-ligand.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6 | 93% H2O/ 7%DMSO-d6 | 95 mM | 7 | ambient mbar | 298 | Bruker AVANCE 700 |
2 | 2D NOESY | 1 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6 | 93% D2O / 7% DMSO-d6 | 95 mM | 7 | ambient mbar | 298 | Bruker AVANCE 700 |
3 | 2D COSY | 1 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6 | 93% H2O/ 7%DMSO-d6 | 95 mM | 7 | ambient mbar | 298 | Bruker AVANCE III 600 |
4 | 2D COSY | 1 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6 | 93% D2O / 7% DMSO-d6 | 95 mM | 7 | ambient mbar | 298 | Bruker AVANCE III 600 |
5 | 2D 1H-13C HSQC aliphatic | 1 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6 | 93% D2O / 7% DMSO-d6 | 95 mM | 7 | ambient mbar | 298 | Bruker AVANCE 700 |
6 | 2D 1H-13C HSQC aromatic | 1 mM DNA 26mer, 70 mM potassium chloride, 25 mM KPi, 0.3 mM DSS, 1.3 mM Auoxo6 | 93% D2O / 7% DMSO-d6 | 95 mM | 7 | ambient mbar | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 600 |
2 | Bruker | AVANCE | 700 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | simulated annealing with cartesian angle dynamics; refinement in explicit water | ARIA |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | 3.2 | Bruker Biospin |
2 | processing | TopSpin | 3.2 | Bruker Biospin |
3 | chemical shift assignment | Sparky | 3.114 | Goddard and Kneller |
4 | peak picking | Sparky | 3.114 | Goddard and Kneller |
5 | data analysis | Sparky | 3.114 | Goddard and Kneller |
6 | refinement | ARIA | 1.2 HJ development version | Linge, O'Donoghue and Nilges |
7 | structure calculation | ARIA | 1.2 HJ development version | Linge, O'Donoghue and Nilges |
8 | structure calculation | CNS | 1.1 | Brunger, Adams, Clore, Gros, Nilges and Read |