8R1X

Solution structure and chemical shift assignments for HMG-D Y12F mutant complexed to a 14:12 dA2 bulge DNA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
2	2D 1H-13C HSQC	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
3	2D 1H-1H NOESY (mixing time = 60 ms)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
4	2D 1H-1H NOESY (mixing time = 150 ms)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
5	3D HNCA	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 500
6	3D HN(CO)CA	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 500
7	3D HNCACB	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 500
8	3D HBHANH	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 500
9	3D HBHA(CO)NH	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 500
10	3D HCCH-COSY	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 500
11	3D HCCH-TOCSY	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 500
12	3D 1H-15N NOESY (mixing time = 150 ms)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
13	3D 1H-13C NOESY aliphatic (mixing time = 150 ms)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
14	3D 1H-13C NOESY aromatic (mixing time = 150 ms)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	95% H2O/5% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
15	2D [13C,15N]-filtered [1H-1H] NOESY (mixing time = 100 ms, with filter elements set to reject 13C and 15N coupled signals in F1 and to accept only 13C coupled signals in F2)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	100% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
16	2D [13C,15N]-filtered [1H-1H] NOESY (mixing time = 200 ms, with filter elements set to reject 13C and 15N coupled signals in F1 and to accept only 13C coupled signals in F2)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	100% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800
17	13C-filtered 13C NOESY-HSQC (mixing time = 150 ms, with filter elements set to reject 13C- and 15N-coupled (protein) signals in F1)	1.8 mM [U-13C; U-15N] HMG-D Y12F, 1.8 mM DNA (5'-D(CPGPAPTPAPTPTPAPAPGPAPGPCPC)-3'), 1.8 mM DNA (5'-D(GPGPCPTPCPAPAPTPAPTPCPG)-3'), 10 mM sodium phosphate, 20 mM sodium chloride, 3 mM sodium azide	100% D2O	83 mM	6.0	1 atm	300	Bruker AVANCE 800

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	500
2	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
molecular dynamics		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	60
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	3.2 and 3.5	Bruker Biospin
2	chemical shift assignment	Sparky	3.115	Goddard
3	structure calculation	X-PLOR NIH	2.28	Schwieters, Kuszewski, Tjandra and Clore
4	refinement	Amber	11	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman

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.