1IV6
Solution Structure of the DNA Complex of Human TRF1
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 3D Sequential assignment protocol; 3D HNHA; 3D_15N_separated_NOESY, 3D_13C_separated_NOESY, 2D NOESY, 2D TOCSY and 2D COSY with or without isotope filtering | 1.5-2.5mM TRF1-DNA complex; 5mM Phosphate buffer with 10mM NaCl | 90% H2O, 10% D2O or 100% D2O | 6.8 | ambient | 305 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 600 |
| 2 | Bruker | DRX | 500 |
| 3 | Bruker | AMX | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| distance geometry/simulated annealing | The structures were generated by 4-dimensional simulated annealing (4D-SA) with program EMBOSS, based on a total of 1341 experimental restraints, 901 and 356 are the NOE derived distance restraints for protein and DNA, respectively, 29 are protein dihedral restraints and 55 are protein-DNA intermolecular restrainTs. In addition, 66 hydrogen bond and 221 ring-to-ring restraints are applied through 4D-SA to maintain the DNA base pair planarity. | EMBOSS |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 2 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | The structures were determined by multi-dimensional heteronuclear -edited and -filtered NMR spectroscopy. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | EMBOSS | 5.0 | Nakai, T, Kidera, A, and Nakamura, H. |
| 2 | structure solution | EMBOSS | 5.0 | Nakai, T, Kidera, A, and Nakamura, H. |
