8TT7
NMR Assignments and Structure for the Dimeric Kinesin Neck Domain
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-15N HSQC | 0.75 mM [U-15N] Kinesin_neck | 90% H2O/10% D2O | 150 mM | 6.1 | 1 atm | 310 | Varian INOVA 600 |
2 | 3D HNCACB | 0.75 mM [U-13C; U-15N] Kinesin_neck | 90% H2O/10% D2O | 150 mM | 6.1 | 1 atm | 310 | Varian INOVA 600 |
3 | 3D HNCA | 0.75 mM [U-13C; U-15N] Kinesin_neck | 90% H2O/10% D2O | 150 mM | 6.1 | 1 atm | 310 | Varian INOVA 600 |
4 | 3D HN(CO)CA | 0.75 mM [U-13C; U-15N] Kinesin_neck | 90% H2O/10% D2O | 150 mM | 6.1 | 1 atm | 310 | Varian INOVA 600 |
5 | 3D 1H-15N TOCSY | 0.75 mM [U-15N] Kinesin_neck | 90% H2O/10% D2O | 150 mM | 6.1 | 1 atm | 310 | Varian INOVA 600 |
6 | 3D 1H-15N NOESY | 0.75 mM [U-15N] Kinesin_neck | 90% H2O/10% D2O | 150 mM | 6.1 | 1 atm | 310 | Varian INOVA 600 |
7 | 2D 1H-13C HSQC | 0.75 mM [U-13C; U-15N] Kinesin_neck | 100% D2O | 150 mM | 6.1 | 1 atm | 310 | Bruker AVANCE NEO 600 |
8 | 3D HCACO | 0.75 mM [U-13C; U-15N] Kinesin_neck | 100% D2O | 150 mM | 6.1 | 1 atm | 310 | Bruker AVANCE 500 |
9 | 3D HCCH-TOCSY | 0.75 mM [U-13C; U-15N] Kinesin_neck | 100% D2O | 150 mM | 6.1 | 1 atm | 310 | Bruker AVANCE NEO 600 |
10 | 3D 1H-13C NOESY | 0.75 mM [U-13C; U-15N] Kinesin_neck | 100% D2O | 150 mM | 6.1 | 1 atm | 310 | Bruker AVANCE NEO 600 |
11 | Hydrogen Exchange N-HSQC | 0.75 mM [U-15N] Kinesin_neck | 100% D2O | 150 mM | 6.1 | 1 atm | 296 | Varian INOVA 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Bruker | AVANCE NEO | 600 |
3 | Bruker | AVANCE | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | sa.inp script of X-Plor NIH tutorial followed by 3 cycles of refine.inp (from X-PLOR NIH). Structures with no violations selected for next round. multiple cycles of prot_sa_refine.inp from this site (https://nesgwiki.chem.buffalo.edu/index.php/Structure_Refinement_Using_XPLOR-NIH) until no violations. Structures have no differences the human eye can see but have better PDB quality bars. | X-PLOR NIH |
NMR Ensemble Information | |
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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 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
5 | processing | In-house / custom | iNMR from MNova | |
6 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
7 | processing | Felix | Accelrys Software Inc. | |
2 | structure calculation | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
3 | chemical shift assignment | CcpNmr Analysis | CCPN | |
4 | peak picking | CcpNmr Analysis | CCPN | |
8 | collection | VnmrJ | Varian | |
9 | collection | TopSpin | Bruker Biospin | |
10 | data analysis | CcpNmr Analysis | CCPN |