2JQ8
Solution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
2 | 3D HNCO | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
3 | 3D HNCA | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
4 | 3D HNCACB | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
5 | 3D HN(CO)CA | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
6 | 3D HN(COCA)CB | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
7 | 2D 1H-1H NOESY | 0.7 mM SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
8 | 3D 1H-13C NOESY | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
9 | 3D 1H-15N NOESY | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
10 | 3D HCCH-TOCSY | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 | |
11 | 3D 1H-15N TOCSY | 0.4 mM [U-99% 13C; U-99% 15N] SMB | 90% H2O/10% D2O | 0 | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | UNITY | 750 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
molecular dynamics | Pronto |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (fewest violations) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | Pronto | Kj r, Andersen and Poulsen | |
2 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
3 | data analysis | Sparky | Goddard | |
4 | structure solution | CYANA | Guntert, Mumenthaler and Wuthrich | |
5 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read |