1KAT

Solution Structure of a Phage-Derived Peptide Antagonist in Complex with Vascular Endothelial Growth Factor

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D_15N-separated_NOESY	0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	90% H2O/10% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	298
2	3D_13C-separated_NOESY	0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	100% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	308
3	3D_15N-separated_NOESY	1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	90% H2O/10% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	318
4	3D_13C-separated_NOESY	1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	100% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	318
5	IPAP_1H_15N_HSQC	0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage	90% H2O/10% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	318
6	IPAP_1H_15N_HSQC	1.0mM U-13C/15N labeled VEGF Dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide, 15mg/ml pf1 phage	90% H2O/10% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	318
7	3D_13C-edited_12C-filtered_NOESY	0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	100% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	308
8	3D_12C-filtered_13C-edited_NOESY	1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	100% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	318
9	HNHB	1.0mM U-13C/15N labeled VEGF dimer + 2.25 mM unlabeled v107; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	90% H2O/10% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	318
10	HMSQC-HA	0.6mM U-13C/15N labeled v107 + 0.45 mM unlabeled VEGF Dimer; 50mM sodium chloride, 20mM phosphate buffer, 0.002% sodium azide	90% H2O/10% D2O	50mM sodium chloride, 20 sodium phosphate	7.0	1 atm	308

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	600
2	Bruker	DRX	800

NMR Refinement
Method	Details	Software
Torsion angle dynamics simulated annealing	The structures are based on 3940 NOE-derived distance restraints, 176 distance restraints from hydrogen bonds, 476 dihedral angle restraints, 146 residual dipolar coupling restraints.	XwinNMR

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	120
Conformers Submitted Total Number	24
Representative Model	9 (closest to the average)

Additional NMR Experimental Information
Details	The structure was determined using triple-resonance NMR spectroscopy

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	XwinNMR	2.6	Bruker, Inc.
2	processing	Felix	98.0	Accelys, Inc.
3	data analysis	XEASY	1.3.13	Bartels, Xia, Billeter, Guntert, Wuthrich
4	structure solution	CNX	2000.1	Accelys, Inc.
5	refinement	CNX	2000.1	Accelys, Inc.

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.