Solution structure of the HMG box DNA-binding domain of human stem cell transcription factor Sox2
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D_15N-separated_NOESY | 0.7 mM [U-100% 13C; U-100% 15N] Sox2, 7 % DTT, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 mM | 6.7 | AMBIENT | 298 | |
| 2 | 3D_13C-separated_NOESY | 0.7 mM [U-100% 13C; U-100% 15N] Sox2, 7 % DTT, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 mM | 6.7 | AMBIENT | 298 | |
| 3 | 3D_13C-separated_NOESY (AROMATIC) | 0.7 mM [U-100% 13C; U-100% 15N] Sox2, 7 % DTT, 95% H2O, 5% D2O | 95% H2O/5% D2O | 100 mM | 6.7 | AMBIENT | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 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. STRUCTURES ARE BASED ON A TOTAL OF 1766 NOE CONSTRAINTS ( 597 INTRA, 423 SEQUENTIAL, 224 MEDIUM and 522 LONG RANGE CONSTRAINTS) AND 197 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS. | CNS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | CNS | Brunger A. T. et.al. | |
