1FZX
NMR SOLUTION STRUCTURE OF THE DNA DODECAMER GGCAAAAAACGG
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 1-12; U-13C/15N | 20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0 | 150 KCl | 7.0 | ambient | 293 | |
2 | DQF-COSY | 1.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 1-12; U-13C/15N | 20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0 | 150 KCl | 7.0 | ambient | 293 | |
3 | HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage) | 3mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) unlabeled sample | 20mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0 | 150 KCl | 7.0 | ambient | 293 | |
4 | HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage) | 1.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 13-24; U-13C/15N | 20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0 | 150 KCl | 7.0 | ambient | 293 | |
5 | HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage) | 1.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 7-12; U-13C/15N | 20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0 | 150 KCl | 7.0 | ambient | 293 | |
6 | HCCHRELAY;HCCHTOCSY;ctHSQC (with and without phage) | 1.5mM d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) nucleotides 19-24; U-13C/15N | 20 mM potassium phosphate, 150mM potassium chloride, 0.5mM EDTA pH 7.0 | 150 KCl | 7.0 | ambient | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 500 |
2 | Bruker | DMX | 600 |
3 | Bruker | DMX | 750 |
NMR Refinement | ||
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Method | Details | Software |
matrix relaxation, simulated annealing with residual dipolar couplings | The structure is based on a total of 434 restraints, 220 NOE derived, 90 dihedral angle, 30 Watson-Crick, and 94 residual dipolar coupling restraints | MARDIGRAS |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (n/a) |
Additional NMR Experimental Information | |
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Details | This structure was determined using 13C-H and 15N-H residual dipolar couplings |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | iterative matrix relaxation | MARDIGRAS | 3.2 | James |
2 | iterative matrix relaxation | CORMA | 5.2 | James |
3 | refinement | X-PLOR | with residual dipolar patch | Brunger, Tjandra |