2KJV
Solution structure and backbone dynamics of the ribosomal protein S6wt
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.8-1.2 mM [U-15N] protein, 20 mM MES, 50 mM sodium chloride | 95% H2O/5% D2O | 6.3 | ambient | 298 | ||
2 | 3D 1H-15N TOCSY | 0.8-1.2 mM [U-15N] protein, 20 mM MES, 50 mM sodium chloride | 95% H2O/5% D2O | 6.3 | ambient | 298 | ||
3 | 3D 1H-15N NOESY | 0.8-1.2 mM [U-15N] protein, 20 mM MES, 50 mM sodium chloride | 95% H2O/5% D2O | 6.3 | ambient | 298 | ||
4 | 3D HNHA | 0.8-1.2 mM [U-15N] protein, 20 mM MES, 50 mM sodium chloride | 95% H2O/5% D2O | 6.3 | ambient | 298 | ||
5 | 2D DQF-COSY | 0.8-1.2 mM protein, 50 mM sodium chloride | 100% D2O | 6.3 | ambient | 298 | ||
6 | 2D 1H-1H TOCSY | 0.8-1.2 mM protein, 50 mM sodium chloride | 100% D2O | 6.3 | ambient | 298 | ||
7 | 2D 1H-1H NOESY | 0.8-1.2 mM protein, 50 mM sodium chloride | 100% D2O | 6.3 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | sa.inp and refine.inp used with slight modifications. | xwinnmr/TOPSPIN |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 300 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | xwinnmr/TOPSPIN | Bruker Biospin | |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | chemical shift assignment | ANSIG | Kraulis | |
4 | data analysis | ANSIG | Kraulis | |
5 | peak picking | ANSIG | Kraulis | |
6 | structure solution | X-PLOR | Brunger | |
7 | geometry optimization | X-PLOR | Brunger | |
8 | refinement | X-PLOR | Brunger | |
9 | data analysis | AQUA | Rullmann, Doreleijers and Kaptein | |
10 | structure solution | ProcheckNMR | Laskowski and MacArthur | |
11 | data analysis | TALOS | Cornilescu, Delaglio and Bax | |
12 | structure solution | MOLMOL | Koradi, Billeter and Wuthrich | |
13 | data analysis | MULDER | P. Padrta & V. Sklenar |