U-box domain of the E3 Ubiquitin Ligase E4B
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 2 | 2D 1H-13C HSQC | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 3 | 2D DQF-COSY | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 4 | 2D 1H-1H NOESY | 1 mM U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 5 | 3D CBCA(CO)NH | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 6 | 3D HNCACB | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 7 | 3D HN(CO)CA | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 8 | 3D H(CCO)NH | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 9 | 3D HCCH-TOCSY | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 10 | 3D 1H-15N NOESY | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 11 | 3D 1H-13C NOESY | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| 12 | 3D HCCH-COSY | 750 uM [U-100% 13C; U-100% 15N] U-box domain of E4B | 90% H2O/10% D2O | 25 | 6.5 | ambient atm | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing, molecular dynamics | Computed through AMBER9 in water, Computed through AMBER9 in water. Single residues in some models have phi-psi angle combinations that are outside the norm. These are found only for residues that lack experimental constraints and which are therefore poorly defined in the structure. | NMRPipe |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | 2009.015.15.35 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 2 | chemical shift assignment | Sparky | 3.113 | Goddard |
| 3 | peak picking | Sparky | 3.113 | Goddard |
| 4 | structure solution | CYANA | 2..1 | Guntert, Mumenthaler and Wuthrich |
| 5 | refinement | Amber | 9 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm |
