2K4J
ArsR DNA Binding Domain
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-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
2 | 3D CBCA(CO)NH | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
3 | 3D CBCANH | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
4 | 3D HCC-TOCSY | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
5 | 3D HHC-TOCSY | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
6 | 3D H(CC)(CO)NH | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
7 | 3D HCC(CO)NH | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
8 | 3D HBHA(CO)NH | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
9 | 3D 1H-15N NOESY | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 | |
10 | 3D 1H-13C NOESY | 0.5 mM [U-100% 13C; U-100% 15N] entity | 90% H2O/10% D2O | 0.56 | 7.6 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
torsion angle dynamics, molecular dynamics | CYANA based refinement, energy minimization with AMBER program | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | geometry optimization | Amber | 9 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm |
2 | structure solution | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
3 | data analysis | CSI | 2.0 | Wishart, DS and Sykes, BD |
4 | structure visualization | MOLMOL | 2K.2 | Koradi, Billeter and Wuthrich |
5 | data analysis | ProcheckNMR | 3.5.4 | Laskowski and MacArthur |
6 | data analysis | Procheck | 3.5.4 | Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho |
7 | processing | TopSpin | 2.0 | Bruker Biospin |
8 | chemical shift assignment | Sparky | 3.114 | Goddard |
9 | peak picking | Sparky | 3.114 | Goddard |
10 | processing | Sparky | 3.114 | Goddard |
11 | data analysis | Insight II | v2005.03 | Accelrys Software Inc. |
12 | refinement | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |