8W0Q
Pembrolizumab CDR-H3 Loop Mimic
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H TOCSY | 5.0 mM Hairpin | 90% H2O/10% DMSO | na | 6.5 | 1 atm | 291 | Varian Varian Mercury500 500 |
| 2 | 2D 1H-1H NOESY | 5.0 mM Hairpin | 90% H2O/10% DMSO | na | 6.5 | 1 atm | 291 | Varian Varian Mercury500 500 |
| 3 | 2D 1H-13C HSQC | 5.0 mM Hairpin | 90% H2O/10% DMSO | na | 6.5 | 1 atm | 291 | Varian Varian Mercury500 500 |
| 4 | 2D DQF-COSY | 5.0 mM Hairpin | 90% H2O/10% DMSO | na | 6.5 | 1 atm | 291 | Bruker Bruker Neo NMR 500 |
| 5 | 2D 1H-15N HSQC | 5.0 mM Hairpin | 90% H2O/10% DMSO | na | 6.5 | 1 atm | 291 | Bruker Bruker AVANCE III 700 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | Varian Mercury500 | 500 |
| 2 | Bruker | Bruker Neo NMR | 500 |
| 3 | Bruker | Bruker AVANCE III | 700 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | from MD snapshots a fixed number of confomers were selected and weighted to maximize reproduction of ensemble-averaged NMR observables | CHARMM |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
| Conformers Calculated Total Number | 53799 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (target function) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | VnmrJ | 4.2 | Varian |
| 5 | processing | TopSpin | 3.2 | Bruker Biospin |
| 2 | structure calculation | CHARMM | c42a2 | B. R. Brooks, C. L. Brooks III, A. D. Mackerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus |
| 4 | peak picking | MestreLab (Mnova / MestReNova / MestReC) | 15.0.0 | Mestrelab |
| 3 | refinement | CHARMM | c42a2 | B. R. Brooks, C. L. Brooks III, A. D. Mackerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus |
