Experiment: 1Y7N

Solution structure of the second PDZ domain of the human neuronal adaptor X11alpha

SOLUTION NMR

NMR Experiment
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
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	800

NMR Refinement
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
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
#	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