Experiment: 2KJH

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7	90% H2O/10% D2O	250	7.4	ambient	298
2	3D HNCACB	0.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7	90% H2O/10% D2O	250	7.4	ambient	298
3	3D CBCA(CO)NH	0.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7	90% H2O/10% D2O	250	7.4	ambient	298
4	2D 1H-15N HSQC	0.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14	90% H2O/10% D2O	250	7.4	ambient	298
5	3D HNCACB	0.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14	90% H2O/10% D2O	250	7.4	ambient	298
6	3D CBCA(CO)NH	0.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14	90% H2O/10% D2O	250	7.4	ambient	298
7	2D 1H-15N HSQC with Cross Saturation	0.35 mM [U-100% 15N; U-99% 2H] UbcH8-15, 0.35 mM Ubiquitin-16, 20 mM sodium phosphate-17, 1 mM EDTA-18, 250 mM sodium chloride-19, 50 mM Arginine-20, 50 mM Glutamic Acid-21	90% H2O/10% D2O	250	7.4	ambient	298
8	2D 1H-15N HSQC with Cross Saturation	0.35 mM UbcH8-22, 0.35 mM [U-100% 15N; U-99% 2H] Ubiquitin-23, 20 mM sodium phosphate-24, 1 mM EDTA-25, 250 mM sodium chloride-26, 50 mM Arginine-27, 50 mM Glutamic Acid-28	90% H2O/10% D2O	250	7.4	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	800

NMR Refinement
Method	Details	Software
torsion angle dynamics, simulated annealing	Semi-rigid body docking using previously determined structures of UbcH8 and ubiquitin; calculated 1000 structures-200 low energy structures selected, Semi-flexible simulated annealing and refinement with explicit water	VnmrJ

NMR Ensemble Information
Conformer Selection Criteria	Structures with the lowest energy in the lowest energy cluster
Conformers Calculated Total Number	200
Conformers Submitted Total Number	16
Representative Model	1 (closest to the mean structure)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	VnmrJ	2.1	Varian
2	processing	NMRPipe	2.1	Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	chemical shift assignment	NMRView	5.2.2	Johnson, One Moon Scientific
4	data analysis	NMRView	5.2.2	Johnson, One Moon Scientific
5	refinement	HADDOCK	2.0	Dominguez, Boelens, Bonvin
6	structure solution	HADDOCK	2.0	Dominguez, Boelens, Bonvin
7	refinement	CNS	1.2	Brunger, Adams, Clore, Gros, Nilges and Read

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 R01GM157729.