2MIT
Solution structure of oxidized dimeric form of human defensin 5
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
2 | 3D HNCA | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
3 | 3D HNCO | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
4 | 3D HCACO | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
5 | 3D HNCACB | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
6 | 3D HCCH-TOCSY | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
7 | 3D C(CO)NH | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
8 | 3D H(CCO)NH | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
9 | 3D HNHB | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
10 | 3D 1H-15N NOESY | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
11 | 3D 1H-13C NOESY | 0.5 mM [U-99% 13C; U-99% 15N] protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
12 | 2D 1H-15N HSQC | 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.3 mM protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 | |
13 | 2D 1H-1H NOESY | 0.3 mM [U-99% 13C; U-99% 15N] protein, 0.3 mM protein | 90% H2O/10% D2O | 0 | 4 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | Avance | 600 |
2 | Varian | Avance | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing, molecular dynamics | Initial structures calculated by minimizing target function. Final CYANA structure refined in explicit water using molecular dynamics. | NMRPipe |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
2 | data analysis | XEASY | Bartels et al. | |
3 | chemical shift assignment | XEASY | Bartels et al. | |
4 | peak picking | XEASY | Bartels et al. | |
5 | chemical shift calculation | CYANA | Guntert, Mumenthaler and Wuthrich | |
6 | structure solution | CYANA | Guntert, Mumenthaler and Wuthrich | |
7 | structure solution | X-PLOR_NIH | Schwieters, Kuszewski, Tjandra and Clore | |
8 | refinement | X-PLOR_NIH | Schwieters, Kuszewski, Tjandra and Clore | |
9 | refinement | WhatIF | Vriend | |
10 | refinement | CYANA | Guntert, Mumenthaler and Wuthrich |