1KDL
Solution structure of the amphipathic domain of YopD from Yersinia
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE | 50% H2O; 10 D2O; 40% TFE | 20 mM SODIUM PHOSPHATE BUFFER | 4.5 | 1 atm | 313 | |
2 | 2D TOCSY | 3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE | 50% H2O; 10 D2O; 40% TFE | 20 mM SODIUM PHOSPHATE BUFFER | 4.5 | 1 atm | 313 | |
3 | DQF-COSY | 3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE | 50% H2O; 10 D2O; 40% TFE | 20 mM SODIUM PHOSPHATE BUFFER | 4.5 | 1 atm | 313 | |
4 | 15N HSQC | 3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE | 50% H2O; 10 D2O; 40% TFE | 20 mM SODIUM PHOSPHATE BUFFER | 4.5 | 1 atm | 313 | |
5 | 13C HSQC | 3.5 MM YOPD(278-300); 20 MM SODIUM PHOSPHATE BUFFER, PH 4.5; 1 MM SODIUM AZIDE | 50% H2O; 10 D2O; 40% TFE | 20 mM SODIUM PHOSPHATE BUFFER | 4.5 | 1 atm | 313 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
2 | Bruker | AMX | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | STANDARD SIMULATED ANNEALING PROTOCOL USING XPLOR 3.851. DIHEDRAL RESTRAINTS WERE OBTAINED WITH TALOS | X-PLOR |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy |
Conformers Calculated Total Number | 150 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (n/a) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 3.851 | Brunger |
2 | data analysis | XwinNMR | 2.6 | Bruker |
3 | iterative matrix relaxation | MARDIGRAS | 3.0 | Borgias |
4 | data analysis | TALOS | 98.040.21.02 | Cornilescu |