2K01
Structure of a locked SDF1 dimer
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_15N-separated_NOESY | 0.620 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 298 | |
| 2 | 3D_13C-separated_NOESY | 0.620 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 298 | |
| 3 | 3D_13C-separated_NOESY (AROMATIC) | 0.620 mM [U-100% 13C; U-100% 15N] CXCL12/SDF1-alpha, 90% H2O, 10% D2O | 90% H2O/10% D2O | 21 | 6.8 | AMBIENT | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT | CXCL12 DIMER STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS., CXCL12/CXCR4 COMPLEX STRUCTURES ARE BASED ON A TOTAL OF 2274 NOE CONSTRAINTS ( 692 INTRA, 312 SEQUENTIAL, 300 MEDIUM, 857 LONG RANGE, AND 113 CXCL12 INTERMONOMER CONSTRAINTS (CXCL12 TO CXCL12), AND 138 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. CONSTRAINT WERE IN ONE ASSIGNED AND VALIDATED IN ONE CXCL12/CXCR4 COMPLEX AND THEN DUPLICATED TO GENERATE A SYMMETRY RELATED CONSTRAINT IN THE SECOND COMPLEX. CONSTRAINT TOTALS LISTED ABOVE INCLUDE CONSTRAINTS FROM BOTH MONOMERS. | Xplor-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 | Xplor-NIH | 2.9.3 | SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. |
| 2 | collection | XwinNMR | 3.5 | Bruker |
| 3 | processing | NMRPipe | 2004 | Delagio,F. et al. |
| 4 | data analysis | XEASY | 1.3 | Eccles, C., Guntert, P., Billeter, M., Wuthrich, K. |
| 5 | data analysis | SPSCAN | 1.1.0 | R.W. Glaser |
| 6 | data analysis | GARANT | 2.1 | C. Bartels |
| 7 | structural calculation | CYANA | 2.1 | Guntert, P. |
