2KEE
Structure of SDF-1/CXCL12
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_15N-separated_NOESY | 1.2 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O | 0.001 mM | 6.8 | AMBIENT | 298 | |
| 2 | 3D_13C-separated_NOESY | 1.2 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O | 0.001 mM | 6.8 | AMBIENT | 298 | |
| 3 | 3D_13C-separated_NOESY (AROMATIC) | 1.2 mM CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O | 0.001 mM | 6.8 | AMBIENT | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, CXCL12 STRUCTURES ARE BASED ON A TOTAL OF 1140 NOE CONSTRAINTS ( 393 INTRA, 239 SEQUENTIAL, 168 MEDIUM, 340 LONG RANGE) AND 50 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. | X-PLOR NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR NIH | 2.9.3 | Schwieters, Kuszewski, Tjandra and Clore |
| 2 | collection | TopSpin | Bruker Biospin | |
| 3 | processing | NMRPipe | 2004 | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |
| 4 | data analysis | XEASY | 1.3 | Bartels et al. |
| 5 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
