1OSW
The Stem of SL1 RNA in HIV-1: Structure and Nucleocapsid Protein Binding for a 1X3 Internal Loop
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3 | 99.996% D2O or 90% D2O, 10% H2O | 25 mM NaCl | 6.3 | ambient | 300 | |
2 | 2D TOCSY | 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3 | 99.996% D2O or 90% D2O, 10% H2O | 25 mM NaCl | 6.3 | ambient | 300 | |
3 | HP-COSY | 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3 | 99.996% D2O or 90% D2O, 10% H2O | 25 mM NaCl | 6.3 | ambient | 300 | |
4 | 2D NOESY | 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3 | 99.996% D2O or 90% D2O, 10% H2O | 25 mM NaCl | 5.5 | ambient | 278 | |
5 | H-C HSQC | 1 mM SL1i RNA; 25mM NaCl, 5mM sodium phosphate, 0.1mM EDTA, 0.01% NaN3 | 99.996% D2O or 90% D2O, 10% H2O | 25 mM NaCl | 6.3 | ambient | 300 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DRX | 600 |
NMR Refinement | ||
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Method | Details | Software |
DYANA followed by molecular dynamics using AMBER | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with acceptable covalent geometry,structures with the least restraint violations,structures with the lowest energy,target function |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 23 |
Representative Model | 17 (closest to the average) |
Additional NMR Experimental Information | |
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Details | Structures were determined using 2D NOESY at different temperatures and mixing times. The last residue, A23, was eliminated from the pdb file due to ambiguity in orientation. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.6 | Bruker |
2 | processing | NMRZ/TRIAD | 6.1 | Tripos |
3 | iterative matrix relaxation | MARDIGRAS | 3.2 | University of California, San Francisco |
4 | structure solution | DYANA | 1.5 | Guntert, P., Mumenthaler, C. and Wuthrich, K. |
5 | refinement | Amber | 5.0 | University of California, San Francisco |