Quantitative characterization of configurational space sampled by HIV-1 nucleocapsid using solution NMR and X-ray scattering
SOLUTION NMR - SOLUTION SCATTERING
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D 1H-15N HSQC
0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride
93% H2O/7% D2O
50 mM
6.5
1 atm
308
Bruker AVANCE 500
2
3D HNCO
0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride
93% H2O/7% D2O
50 mM
6.5
1 atm
308
Bruker AVANCE 500
3
3D HNCA
0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride
93% H2O/7% D2O
50 mM
6.5
1 atm
308
Bruker AVANCE 500
4
3D HNCACB
0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride
93% H2O/7% D2O
50 mM
6.5
1 atm
308
Bruker AVANCE 500
5
2D ARTSY
0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 5 % neutral bicelles
93% H2O/7% D2O
50 mM
6.5
1 atm
308
Bruker AVANCE 800
6
3D Quntitaive HNCO - NC'
0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 5 % neutral bicelles
93% H2O/7% D2O
50 mM
6.5
1 atm
308
Bruker AVANCE 500
7
3D Quntitaive HNCO - CaC'
0.2 mM [U-13C; U-15N; U-2H] Nucleocapsid protein of human immunodeficiency virus 1 (HIV-1), 50 mM sodium chloride, 20 mM sodium phosphate, 1 mM Dithiothreitol, 0.1 mM zinc chloride, 5 % neutral bicelles
93% H2O/7% D2O
50 mM
6.5
1 atm
308
Bruker AVANCE 500
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
500
2
Bruker
AVANCE
800
NMR Refinement
Method
Details
Software
simulated annealing
Xplor-NIH
NMR Ensemble Information
Conformer Selection Criteria
structures with the lowest energy
Conformers Calculated Total Number
100
Conformers Submitted Total Number
21
Representative Model
all (lowest energy)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
refinement
Xplor-NIH
2.41
C. D. Schwieters, J. J. Kuszewski, N. Tjandra, G. M. Clore
2
chemical shift assignment
Analysis
2.2.2
W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon, M. Llinas, E. L. Ulrich, J. L. Markley, J. Ionides, E. D. Laue
3
peak picking
Analysis
2.2.2
W. F. Vranken, W. Boucher, T. J. Stevens, R. H. Fogh, A. Pajon, M. Llinas, E. L. Ulrich, J. L. Markley, J. Ionides, E. D. Laue
