Solution structure of the HIV-1 nucleocapsid (NCp7(12-55)) complexed with the DNA (-) Primer Binding Site
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D TOCSY | 1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O | 90% H2O/10% D2O | 1mM protein, 1mM oligonucleotide | 6.5 | ambient | 283 | |
| 2 | 2D NOESY | 1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O | 90% H2O/10% D2O | 1mM protein, 1mM oligonucleotide | 6.5 | ambient | 283 | |
| 3 | 2D TOCSY | 1mM NCp7(12-55), 1mM DP(-)PBS | 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2 | 1mM protein, 1mM oligonucleotide | 6.5 | ambient | 283 | |
| 4 | 2D NOESY | 1mM NCp7(12-55), 1mM DP(-)PBS | 90% H2O, 10% D2O, 30mM NaCl, 0.2mM MgCl2 | 1mM protein, 1mM oligonucleotide | 6.5 | ambient | 283 | |
| 5 | 2D TOCSY | 1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O | 90% H2O/10% D2O | 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2 | 6.5 | ambient | 283 | |
| 6 | 2D NOESY | 1mM NCp7(12-55), 1mM DP(-)PBS, 90% H2O, 10% D2O | 90% H2O/10% D2O | 1mM protein, 1mM oligonucleotide, 30mM NaCl, 0.2mM MgCl2 | 6.5 | ambient | 283 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| restrained molecular dynamics restrained simulated annealing energy minimization | structures are based on 705 restraints (NOE derived distance constraints) | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 3.0 | Bruker |
| 2 | processing | XwinNMR | 3.0 | Bruker |
| 3 | refinement | Discover | 2.98 | Accelrys |
