6QF8
Solution NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D CNH-NOESY | 1.0 mM [U-99% 13C; U-99% 15N] human ubiquitin, 40 mM sodium phosphate | 95% H2O/5% D2O | 100 mM | 5.8 | 1 atm | 298 | Bruker AVANCE III 800 |
2 | 3D C(CO)NH | 1.0 mM [U-99% 13C; U-99% 15N] human ubiquitin, 40 mM sodium phosphate | 95% H2O/5% D2O | 100 mM | 5.8 | 1 atm | 298 | Bruker AVANCE III 600 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
2 | Bruker | AVANCE III | 800 |
3 | Bruker | AVANCE III | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
R-factor based frame picking | frames selected from unrestrained MD simulations to minimise the overall NOESY-based R-factor | CoMAND |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | NOESY-based R-factor selection |
Conformers Calculated Total Number | 10000 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
6 | collection | TopSpin | Bruker Biospin | |
1 | chemical shift assignment | Sparky | Goddard | |
3 | structure calculation | Rosetta | 3.6 | Das & Baker |
4 | refinement | NAMD 2.12 | University of Illinois | |
2 | refinement | Shine | Riss & Coles | |
5 | refinement | CoMAND | in house |