NMR-based docking model of GrxS14-BolA2 apo-heterodimer from Arabidopsis thaliana
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 0.12 mM [U-100% 15N] BolA2, 0.012-0.24 mM GrxS14 | 90% H2O/10% D2O | 0.05 | 7 | ambient | 298 | |
| 2 | 2D 1H-15N HSQC | 0.12 mM [U-100% 15N] GrxS14, 0.012-0.24 mM BolA2 | 90% H2O/10% D2O | 0.05 | 7 | ambient | 298 | |
| 3 | 2D 1H-15N HSQC | 0.12 mM [U-100% 15N] GrxS14 | 90% H2O/10% D2O | 0.05 | 7 | ambient | 298 | |
| 4 | 2D 1H-15N HSQC | 0.12 mM [U-100% 15N] BolA2 | 90% H2O/10% D2O | 0.05 | 7 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics, energy minimization | Energy minimization using the YASARA force field. The structure was moved to a nearby (local) minimum, with removal of clashes and small errors. | NMRView |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | all calculated structures submitted |
| Conformers Calculated Total Number | 1 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | peak picking | NMRView | Johnson, One Moon Scientific | |
| 2 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
| 3 | structure solution | GRAMM-X_Protein-Protein_Docking_Web_Server | 1.2.0 | Tovchigrechko |
| 4 | geometry optimization | YASARA_Energy_Minimization_Server | Krieger | |
| 5 | refinement | YASARA_Energy_Minimization_Server | Krieger | |
| 6 | refinement | GRAMM-X_Protein-Protein_Docking_Web_Server | Tovchigrechko | |
