1S4G

Somatomedin-B Domain of human plasma vitronectin.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	Isolated from human plasma vitronectin by CNBr cleavage		low	4.4		298
2	2D TOCSY	Isolated from human plasma vitronectin by CNBr cleavage		low	4.4		298
3	DQF-COSY	Isolated from human plasma vitronectin by CNBr cleavage		low	4.4		298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600

NMR Refinement
Method	Details	Software
simulated annealing	NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper limits involving methyl protons, 0.5 for methylene protons and 2.3 for degenerate Hd and He protons of tyrosines and phenylalanines. Also, a 0.2 was added to the upper limits of NOEs involving amide protons. Backbone F angles were restrained to -120 50 for 3JHNHa = 8-9 Hz, and -120 40 for JHNHa > 9Hz. A restraint of 100 80 was also applied to F angle for residues that show stronger NHi-Hai-1 NOE than the intraresidue NH-Ha NOE. A total of 329 NOE restraints and 18 F restraints were used in structure determination. Random structures were generated by subjecting the peptide to an initial 10000-step minimization at 298K. The temperature was then raised gradually to 1000K during a 1000 step dynamics simulation. The peptide was subjected to minimization and a 10ps dynamics at 1000K. The NMR-derived restraints were then imposed on the peptide and the peptide was slowly annealed to 298K in a 100ps trajectory. Finally, the structures were subjected to further minimization at 298K. The force constant for the distance restraints was 100 kcal/mol 2 and the dielectric constant was 4.	Discover

NMR Ensemble Information
Conformer Selection Criteria	structures with favorable non-bond energy
Conformers Calculated Total Number	60
Conformers Submitted Total Number	20
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Discover	Discover 3 (2000)	Accelrys (San Diego, CA)
2	processing	Felix	Felix 2000	Accelrys (San Diego, CA)
3	data analysis	Sparky		Goddard, T.D. and Kneller, D.G.
4	data analysis	MOLMOL		Koradi, R., Billeter, M., and Wuthrich, K.
5	data analysis	PROCHECK		Laskowski, R.A., Rullmann, J.A.C., MacArthur, M.W., Kaptein, R., and Thorntorn, J.M.
6	refinement	Discover	Discover 3 (2000)	Accelrys (San Diego, CA)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.