2JMJ

NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	0.52 mM [U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
2	2D 1H-13C HSQC	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
3	2D 1H-1H TOCSY filter	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
4	2D 1H-1H NOESY filter	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
5	3D HNCA	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
6	3D HNCACB	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
7	3D HBHA(CO)NH	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
8	3D HCCH-TOCSY	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
9	3D 1H-15N NOESY	0.52 mM [U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
10	3D 1H-13C NOESY	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
11	3D 1H-15N NOESY filter	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20
12	3D 1H-13C NOESY filter	0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O	90% H2O/10% D2O	50	7.5	ambient	20

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

NMR Refinement
Method	Details	Software
torsion angle dynamics		X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	20
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
2	data analysis	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
3	data analysis	TALOS		Cornilescu, Delaglio and Bax
4	collection	TopSpin		Bruker Biospin
5	processing	TopSpin		Bruker Biospin
6	chemical shift assignment	CARA		Keller and Wuthrich
7	data analysis	CARA		Keller and Wuthrich
8	solution structure	CARA		Keller and Wuthrich
9	refinement	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore

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.