2LI9
Metal binding domain of rat beta-amyloid
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C HSQC | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
2 | 2D DQF-COSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 90% H2O/10% D2O | 10 | 7.1 | ambient | 278 | |
3 | 2D DQF-COSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
4 | 2D 1H-1H NOESY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 90% H2O/10% D2O | 10 | 7.1 | ambient | 278 | |
5 | 2D 1H-1H NOESY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
6 | 2D 1H-1H TOCSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 100% D2O | 10 | 7.1 | ambient | 278 | |
7 | 2D 1H-1H TOCSY | 5 mM protein_1, 8 mM Zinc cloride, 20 mM [U-100% 2H] TRIS, 0.1 % sodium azide | 90% H2O/10% D2O | 10 | 7.1 | ambient | 278 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | Avance | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, QM/MM geometry optimization | simulation in explicit water environment | TOPSPIN |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 40 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | TOPSPIN | Bruker Biospin | |
2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | data analysis | SPARKY | Goddard | |
4 | data analysis | AngleSearch | V. Polshakov | |
5 | structure solution | GROMACS | 3.3.1 | Van Der Spoel et al. |
6 | geometry optimization | GROMACS/CPMD | Biswas & Gogonea | |
7 | data analysis | ProcheckNMR | Laskowski and MacArthur | |
8 | data analysis | InsightII | Accelrys Software Inc. | |
9 | refinement | GROMACS | Van Der Spoel et al. | |
10 | refinement | GROMACS/CPMD | Biswas & Gogonea |