Experiment: 7EH3

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
2	2D 1H-15N TROSY	290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O	95% H2O/5% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
3	3D CBCANH	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
4	3D CBCA(CO)NH	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
5	3D HNCA	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
6	3D C(CO)NH	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
7	3D H(CCO)NH	290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O	95% H2O/5% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
8	3D HBHA(CO)NH	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
9	3D HNCO	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
10	3D HN(CA)CO	250 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O, 19.5 mM TRIS, 21 mM sodium chloride	95% H2O/5% D2O	21 (sodium chloride) mM	6.95	1 atm	298	Bruker AVANCE III 600
11	2D 1H-1H TOCSY	190 uM Nb23, 10 mM sodium phosphate, 5 % D2O, 6.3 mM sodium chloride	95% H2O/5% D2O	6.3 mM	6.95	1 atm	298	Bruker AVANCE III 600
12	3D 1H-15N NOESY	290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O	95% H2O/5% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
13	2D HBCBCGCDHD	190 uM Nb23, 10 mM sodium phosphate, 100 % D2O	100% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
14	2D HBCBCGCDCEHE	190 uM Nb23, 10 mM sodium phosphate, 100 % D2O	100% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
15	2D 1H-1H NOESY	100 uM Nb23, 10 mM sodium phosphate, 100 % D2O, 20 mM sodium chloride	100% D2O	20 mM	6.95	1 atm	298	Bruker AVANCE III 600
16	3D 1H-13C NOESY aliphatic	190 uM Nb23, 10 mM sodium phosphate, 100 % D2O	100% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
17	3D 1H-13C NOESY aromatic	190 uM Nb23, 10 mM sodium phosphate, 100 % D2O	100% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
18	2D 1H-13C HSQC	290 uM [U-10% 13C; U-100% 15N] Nb23, 10 mM sodium phosphate, 5 % D2O	95% H2O/5% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600
19	2D 1H-15N HSQC	190 uM Nb23, 10 mM sodium phosphate, 100 % D2O	100% D2O	0 mM	6.95	1 atm	298	Bruker AVANCE III 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	600

NMR Refinement
Method	Details	Software
energy minimization		NAMD

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	20
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	peak picking	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
3	chemical shift assignment	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
4	data analysis	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
5	chemical shift calculation	NMRFAM-SPARKY		Lee W, Tonelli M, Markley JL
6	structure calculation	CS-ROSETTA		Shen, Vernon, Baker and Bax
7	geometry optimization	MolProbity		Richardson
8	data analysis	MolProbity		Richardson
9	data analysis	PONDEROSA		Lee W, Kim JH, Westler WM, Markley JL
10	refinement	PONDEROSA		Lee W, Kim JH, Westler WM, Markley JL
11	structure calculation	PONDEROSA		Lee W, Kim JH, Westler WM, Markley JL
12	geometry optimization	PONDEROSA		Lee W, Kim JH, Westler WM, Markley JL
13	refinement	PONDEROSA-C/S		Lee W, Stark JL, Markley JL
14	structure calculation	PONDEROSA-C/S		Lee W, Stark JL, Markley JL
15	geometry optimization	PROCHECK / PROCHECK-NMR		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton
18	geometry optimization	PyMOL		The PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLC
17	data analysis	PyMOL		The PyMOL Molecular Graphics System, Version 2.0 Schrodinger, LLC
16	data analysis	PROCHECK / PROCHECK-NMR		Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton
19	geometry optimization	TALOS-N		Yang S, Bax A
20	processing	TopSpin		Bruker Biospin
21	data analysis	TopSpin		Bruker Biospin
22	refinement	NAMD	NAMD2	Kale L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shi- nozaki A, Varadarajan K, Schulten K

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.

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7EH3

Structure of Nanobody Nb23 in solution using NMR spectroscopy