1J9V
Solution structure of a lactam analogue (DabD) of HIV gp41 600-612 loop.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | DQF-COSY | 3,5 mM peptide in 500ul DMSO-D6 | DMSO-D6 | ambient | 298 | |||
2 | 2D NOESY | 3,5 mM peptide in 500ul DMSO-D6 | DMSO-D6 | ambient | 298 | |||
3 | TOCSY |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 400 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
Torsion angle dinamics, molecular dynamics, energy minimization. | 50 INITIAL RANDOM STRUCTURES WERE GENERATED USING SIMULATED ANNEALING IN DYANA SOFTWARE, FOLLOWED BY 500PS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K, 200 PS MD UNDER NMR RESTRAINTS AND 750 STEPS CONJUGATED GRADIENT EM USING DISCOVER OF MSI SOFTWARE | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 49 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques. Different NOESY experiments with mixing times from 80 ms to 800 ms were recorded, in order to determined the best conditions avoiding spin diffusion. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.6 | Bruker GMBH |
2 | processing | XwinNMR | 2.6 | Bruker GMBH |
3 | data analysis | XEASY | 1.2 | Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10 |
4 | refinement | DYANA | 1.5 | Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol. 273, 283-298 |
5 | refinement | Discover | 3 | Molecular Simulation Inc. San Diego |