2LQR
NMR structure of Ig3 domain of palladin
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 50 mM TRIS-maleate, 150 mM NaCl, 2 mM DTT, 0.01 % sodium azide, 10 % D2O | 90% H2O/10% D2O | 150 | 6.0 | ambient | 298 | |
2 | 3D 1H-15N NOESY | 50 mM TRIS-maleate, 150 mM NaCl, 2 mM DTT, 0.01 % sodium azide, 10 % D2O | 90% H2O/10% D2O | 150 | 6.0 | ambient | 298 | |
3 | 3D 1H-13C NOESY aliphatic | 50 mM TRIS-maleate, 150 mM NaCl, 2 mM DTT, 0.01 % sodium azide, 10 % D2O | 90% H2O/10% D2O | 150 | 6.0 | ambient | 298 | |
4 | 3D 1H-13C NOESY aromatic | 50 mM TRIS-maleate, 150 mM NaCl, 2 mM DTT, 0.01 % sodium azide, 10 % D2O | 90% H2O/10% D2O | 150 | 6.0 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 700 |
2 | Varian | INOVA | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing, torsion angle dynamics, matrix relaxation | RASREC method has six stages that cycle between generating Rosetta fragments, producing low energy models, and biasing conformational search space towards low energy space | NMRView |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (fewest violations) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | peak picking | NMRView | Johnson, One Moon Scientific | |
2 | processing | NMRView | Johnson, One Moon Scientific | |
3 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
4 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
5 | structure solution | CYANA | 2.2 | Guntert, Mumenthaler and Wuthrich |
6 | data analysis | PSVS | Bhattacharya and Montelione | |
7 | refinement | Rosetta | RASREC | O.F. Lange and D. Baker |
8 | refinement | CYANA | Guntert, Mumenthaler and Wuthrich |