2KVN
Phi29 E-loop hairpin
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C HSQC | 1 mM RNA, 10 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM sodium-EDTA | 100% D2O | 5.5 | ambient | 293 | ||
2 | 2D DQF-COSY | 1 mM RNA, 10 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM sodium-EDTA | 100% D2O | 5.5 | ambient | 274 | ||
3 | 2D 1H-1H NOESY | 1 mM RNA, 10 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM sodium-EDTA | 100% D2O | 5.5 | ambient | 274 | ||
4 | 2D 1H-1H NOESY | 1 mM RNA, 10 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM sodium-EDTA | 100% D2O | 5.5 | ambient | 293 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 500 |
2 | Varian | INOVA | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
DGSA-distance geometry simulated annealing | CNS |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with no restraint violations |
Conformers Calculated Total Number | 132 |
Conformers Submitted Total Number | 30 |
Representative Model | 1 (minimized average structure) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | geometry optimization | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | refinement | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
3 | chemical shift assignment | Sparky | Goddard | |
4 | chemical shift calculation | Sparky | Goddard | |
5 | peak picking | Sparky | Goddard | |
6 | data analysis | Sparky | Goddard | |
7 | processing | Sparky | Goddard | |
8 | collection | VNMR | Varian | |
9 | data analysis | VNMR | Varian | |
10 | processing | VNMR | Varian | |
11 | data analysis | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm | |
12 | data analysis | PyMOL | Delano |