6CLZ
MT1-MMP HPX domain with Blade 4 Loop Bound to Nanodiscs
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | HMQC | 20 mM Tris-HCl, 300 mM NaCl, 0.02 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 90 uM 2H, 13C, 15N MT1-MMP hemopexin-like domain, 180 uM MSP1D1, 14.4 mM PX4 | 93% H2O/7% D2O | 300 mM | 7.2 | 1 atm | 303 | Bruker AVANCE III 800 |
| 2 | TROSY | 20 mM Tris-HCl, 300 mM NaCl, 0.02 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 90 uM 2H, 13C, 15N MT1-MMP hemopexin-like domain, 180 uM MSP1D1, 14.4 mM PX4 | 93% H2O/7% D2O | 300 mM | 7.2 | 1 atm | 303 | Bruker AVANCE III 800 |
| 3 | CPMG-HMQC | 20 mM Tris-HCl, 300 mM NaCl, 0.02 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 90 uM 2H, 13C, 15N MT1-MMP hemopexin-like domain, 180 uM MSP1D1, 14.4 mM PX4 | 93% H2O/7% D2O | 300 mM | 7.2 | 1 atm | 303 | Bruker AVANCE III 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | restrained molecular dynamics | NAMD |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 500 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | TopSpin | 3.2 | Bruker |
| 2 | data analysis | Analysis | 2.4 | CCPN |
| 3 | structure calculation | HADDOCK | HADDOCK2.1 | Bonvin |
| 4 | structure calculation | NAMD | NAMD2.1 with CUDA GPU processing | Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign |
| 5 | refinement | NAMD | NAMD2.1 with CUDA GPU processing | Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign |
