2HZ8

QM/MM structure refined from NMR-structure of a single chain diiron protein

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_13C-separated_NOESY	2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O	95% water, 5% D20	10 mM NaCl	6.0	ambient	308
2	3D_15N-separated_NOESY	2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O	95% water, 5% D20	10 mM NaCl	6.0	ambient	308
3	4D_13C/15N-separated_NOESY	2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O	95% water, 5% D20	10 mM NaCl	6.0	ambient	308
4	4D_13C-separated_NOESY	2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O	95% water, 5% D20	10 mM NaCl	6.0	ambient	308
5	HNHA	2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O	95% water, 5% D20	10 mM NaCl	6.0	ambient	308
6	IPAP-15N HSQC	2 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O DIHEXANOYLPHOSPHATIDYLCHOLINE, DIMYRISTOYLPHOSPHATIDYLCHOLINE	95% water, 5% D20

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	750
2	Varian	INOVA	500

NMR Refinement
Method	Details	Software
1. Step: Classical Molecular dynamics simulation starting from NMR-structure, using non-bonded model for metal-site. 2. step: QM/MM MD for relaxation of local frustrations at the metal site.	Average over last ps of 5ps QM/MM trajectory. Two metal-site water molecules are included in the average. Other solvent molecules and counter ions are excluded. Atoms included in the QM-part are indicated with a value of 1 in the beta-factor column, whereas atoms in the MM-part are indicated with a value of 0 in the beta-factor column.	CNS

NMR Ensemble Information
Conformer Selection Criteria	dynamical average of 300K trajectory
Conformers Calculated Total Number	1
Conformers Submitted Total Number	1

Additional NMR Experimental Information
Details	The structure was first determined using triple-resonance spectrscopy. The structure was then further refined using classical MD followed by 5 ps of Car Parrinello hybrid QM/MM dynamics.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	CNS	1.1	A. Brunger, P. Adams, M. Clore, P.Gros, M. Nilges, and R. Reed
2	processing	NMRPipe	linux9	F. Delaglio, S. Grzesiek, A. Bax, Geerten, and W. Vuister
3	data analysis	Sparky	3.110	T.D. Goddard and D.G. Kneller
4	collection	VNMR	6.1b	P. Nicholas, D. Fushman, V. Ruchinsky, and D. Cowburn
5	refinement	NAMD	version 2.6	Laxmikant, K, Skeel, R, Bhandarkar, M, Brunner, R, Gursoy, A, Krawetz, N, Phillips, J, Shinozaki, A, Varadarajan, K,Schulten, K
6	refinement	Amber	version 8	Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., Woods, R. J.
7	refinement	QM/MM	(Version 3.10), based on CPMD and GROMOS	CPMD: Hutter, J, Alavi, A, Deutsch, T, Ballone, P, Bernasconi, M, Focher, P, Goedecker, S; GROMOS Scott WRP, Huhnenberger, PH, Tironi, TG, Mark, AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF: Laio, A., VandeVondele, J., Rothlisberger, U.