2MC2
X-ray crystallography-solution NMR hybrid structure of mouse RyR2 domain A
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 | 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT | 90% H2O/10% D2O | 0.328 | 7 | ambient | 288 | |
2 | 3D CBCA(CO)NH | 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT | 90% H2O/10% D2O | 0.328 | 7 | ambient | 288 | |
3 | 3D HNCACB | 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT | 90% H2O/10% D2O | 0.328 | 7 | ambient | 288 | |
4 | 3D HNCO | 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT | 90% H2O/10% D2O | 0.328 | 7 | ambient | 288 | |
5 | 3D HNCA | 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT | 90% H2O/10% D2O | 0.328 | 7 | ambient | 288 | |
6 | 3D HN(CO)CA | 0.4 mM [U-13C; U-15N; U-2H] RyR2, 20 mM sodium phosphate, 300 mM sodium chloride, 2 mM TCEP, 5 mM DTT | 90% H2O/10% D2O | 0.328 | 7 | ambient | 288 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing | The RECOORD scripts [Proteins. 2005 Jun 1;59(4):662-72] were employed to reanneal and refine the structure with the addition of the new NMR restraints. PDB entry 3IM5 was used as the starting structure for refinement. | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | TROSY pulse sequences were employed. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
2 | chemical shift assignment | XEASY | Bartels et al. | |
3 | peak picking | XEASY | Bartels et al. | |
4 | data analysis | TALOS | Cornilescu, Delaglio and Bax | |
5 | geometry optimization | TALOS | Cornilescu, Delaglio and Bax | |
6 | chemical shift calculation | TALOS | Cornilescu, Delaglio and Bax | |
7 | refinement | CNS | Brunger, Adams, Clore, Gros, Nilges and Read | |
8 | structure solution | CNS | Brunger, Adams, Clore, Gros, Nilges and Read |