1MZI | pdb_00001mzi

Solution ensemble structures of HIV-1 gp41 2F5 mAb epitope

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.5mM peptide, 50mM phosphate buffer, pH 6.5	95% H2O/5% D2O	50mM phosphate buffer	6.5	ambient	278
2	2D TOCSY	1.5mM peptide, 50mM phosphate buffer, pH 6.5	95% H2O/5% D2O	50mM phosphate buffer	6.5	ambient	278
3	PE-COSY	1.5mM peptide, 50mM phosphate buffer, pH 6.5	95% H2O/5% D2O	50mM phosphate buffer	6.5	ambient	278
4	HSQC (1H-13C)-Dipsi-2(1H)	1.5mM peptide, 50mM phosphate buffer, pH 6.5	95% H2O/5% D2O	50mM phosphate buffer	6.5	ambient	278
5	HMQC (1H-15N) jr	1.5mM peptide, 50mM phosphate buffer, pH 6.5	95% H2O/5% D2O	50mM phosphate buffer	6.5	ambient	278

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600
2	Bruker	DRX	500

NMR Refinement
Method	Details	Software
Ensemble generation with MEDUSA, Clustering analysis with NMRCLUST, Statistical analysis of the ensemble with NAMFIS		NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	Base set ensemble representative of the conformational space experimentally allowed
Conformers Calculated Total Number	6400
Conformers Submitted Total Number	81

Additional NMR Experimental Information

Details

Distance restraints were determined using NOESY build-up curves. The coupling constants were determined using phase sensitive COSY and TOCSY experiments. E threshold cutoff and deltaE allowance for MEDUSA were 600 and 100 kCal/mol respectively Clustering was performed with a cutoff of 1.0Angstrom A conformer was defined as different if either phi or psi angle for at least one aminoacid was differing by >15 degrees

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	NMRPipe	2001	Delaglio, F.
2	data analysis	NMRView	2001	Johnson, B.
3	refinement	DGII	MSI	MSI, Inc
4	refinement	NAMFIS	1.0	Cicero D.
5	refinement	MEDUSA	in home	Brushweiler R.
6	refinement	NMRCLUST	1.2	Kelley