1MZI
Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 95% H2O/5% D2O | 50mM phosphate buffer | 6.5 | ambient | 278 | |
2 | 2D TOCSY | 1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 95% H2O/5% D2O | 50mM phosphate buffer | 6.5 | ambient | 278 | |
3 | PE-COSY | 1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 95% H2O/5% D2O | 50mM phosphate buffer | 6.5 | ambient | 278 | |
4 | HSQC (1H-13C)-Dipsi-2(1H) | 1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 95% H2O/5% D2O | 50mM phosphate buffer | 6.5 | ambient | 278 | |
5 | HMQC (1H-15N) jr | 1.5mM peptide, 50mM phosphate buffer, pH 6.5 | 95% H2O/5% D2O | 50mM phosphate buffer | 6.5 | ambient | 278 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 600 |
2 | Bruker | DRX | 500 |
NMR Refinement | ||
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Method | Details | Software |
Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFIS | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | Base set ensemble representative of the conformational space experimentally allowed |
Conformers Calculated Total Number | 6400 |
Conformers Submitted Total Number | 81 |
Additional NMR Experimental Information | |
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Details | Distance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance for MEDUSA were 600 and 100 kCal/mol respectively Clustering was performed with a cutoff of 1.0Angstrom A conformer was defined as different if either phi or psi angle for at least one aminoacid was differing by >15 degrees |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | NMRPipe | 2001 | Delaglio, F. |
2 | data analysis | NMRView | 2001 | Johnson, B. |
3 | refinement | DGII | MSI | MSI, Inc |
4 | refinement | NAMFIS | 1.0 | Cicero D. |
5 | refinement | MEDUSA | in home | Brushweiler R. |
6 | refinement | NMRCLUST | 1.2 | Kelley |