1IV6
Solution Structure of the DNA Complex of Human TRF1
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DMX | 600 |
2 | Bruker | DRX | 500 |
3 | Bruker | AMX | 500 |
NMR Refinement | ||
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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 | |
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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 | |
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Details | The structures were determined by multi-dimensional heteronuclear -edited and -filtered NMR spectroscopy. |
Computation: NMR Software | ||||
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# | 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. |