1Y7N
Solution structure of the second PDZ domain of the human neuronal adaptor X11alpha
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_15N-separated_NOESY | 1.2mM PDZ2a U-15N,13C; 10mM sodium phosphate buffer; pH 6.7; 95% H2O; 5% D2O | 95% H2O/5% D2O | 10mM | 6.7 | 1 atm | 290 | |
2 | 3D_13C-separated_NOESY | 1.2mM PDZ2a U-15N,13C; 10mM sodium phosphate buffer; pH 6.7; 95% H2O; 5% D2O | 95% H2O/5% D2O | 10mM | 6.7 | 1 atm | 290 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, molecular dynamics simulation, torsion angle dynamics, distance and dihedral angle restraints | The final structure calculations with CYANA were started from 100 conformers with random torsion angle values. Simulated annealing with 10,000 time steps per conformer was done using the DYANA torsion angle dynamics algorithm. Using the FormatConverter, developed as part of the Collaborative Computing Project for the NMR Community (CCPN), the distance and dihedral angle restraints were converted to the X-PLOR restraint format. Subsequently the 100 generated structures were refined using a sh rt restrained molecular dynamics simulation in explicit solvent in the program XPLOR-NIH. Of these, the 20 lowest energy structures were selected to form the final ensemble. | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | 2002 release | F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax |
2 | data analysis | CARA | 1.1.8 | R.L.J. Keller |
3 | structure solution | CYANA | 1.0 | P. Guntert |
4 | refinement | X-PLOR | 2.9.6 | |
5 | collection | VNMR |