5TBN

Solution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.5 mM [U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
2	3D 1H-15N NOESY	1.5 mM [U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
3	2D 1H-13C HSQC	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
4	3D HNCACB	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
5	3D CBCA(CO)NH	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
6	3D HNCO	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
7	3D NH(CA)CO	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
8	3D HBHA(CO)NH	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
9	3D CCH-TOCSY	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
10	3D 1H-15N NOESY	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
11	3D 1H-13C NOESY aliphatic	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
12	3D 1H-13C NOESY aromatic	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
13	3D 13C,15N-filtered, 13C/15N-edited NOESY	1.5 mM [U-13C; U-15N] PHF20 PHD domain, 6.0 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
14	2D 1H-13C HSQC	2 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
15	2D 1H-1H NOESY	2 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700
16	2D 1H-1H COSY	2 mM H3K4me2 peptide, 25 mM sodium phosphate, 0.3 mM DSS, 1.5 mM sodium azide	90% H2O/10% D2O	20 mM sodium phosphate mM	7.0	101325 Pa	298	Bruker AVANCE III 700

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE III	700

NMR Refinement
Method	Details	Software
simulated annealing		Amber

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

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin		Bruker Biospin
2	chemical shift assignment	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5	chemical shift assignment	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	chemical shift assignment	NMRView		Johnson, One Moon Scientific
4	peak picking	NMRView		Johnson, One Moon Scientific
6	chemical shift assignment	SANE		Duggan, Legge, Dyson & Wright
7	processing	NMRDraw		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
8	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
10	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
9	refinement	Amber	14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman
11	data analysis	TALOS		Cornilescu, Delaglio and Bax

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.