Experiment: 2LEV

SOLUTION NMR - SOLUTION SCATTERING

Solution Scattering Data Acquistion	1
Scattering Type	x-ray
Radiation/Neutron Source	DESY-EMBL HAMBURG OUTSTATION
Synchrotron	N
Beamline Type	X33
Detector Type	2D PHOTON COUNTING PILATUS 1M PIXEL
Detector Manufacturer Details
Temperature (K)	298
pH	5.7
Numer of Time Frames Used	4
Protein Concentration Range (mg/mL)	3.6 - 7.3
Sample Buffer	20mM sodium phosphate, 150mM NaCl, 0.2mM EDTA, 0.01%NaN3
Data Reduction Software	PRIMUS, GNOM, CRYSOL
Guiner Mean Radius Of Gyration (nm)	1.82
Sigma Mean Radius Of Gyration	0.01
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)	5.3

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-15N HSQC	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
2	2D 1H-13C HSQC aliphatic	1 mM [U-10% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 % (w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
3	3D HNCACB	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
4	3D CBCA(CO)NH	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
5	3D H(CCO)NH	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
6	3D HCCH-TOCSY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	100% D2O	150	5.7	ambient	298
7	3D HNHA	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
8	3D 1H-15N TOCSY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
9	3D 1H-15N NOESY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
10	3D 1H-13C NOESY aliphatic	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
11	3D 1H-13C NOESY aliphatic	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	100% D2O	150	5.7	ambient	298
12	2D 1H-1H (13C-ed) NOESY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	100% D2O	150	5.7	ambient	298
13	2D 1H-1H NOESY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
14	2D 1H-1H (13C-fil) NOESY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	100% D2O	150	5.7	ambient	298
15	2D 1H-1H (15N/13C-fil) NOESY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
16	3D 15N/13C-fil/13c-ed- NOESY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	90% H2O/10% D2O	150	5.7	ambient	298
17	2D 1H-1H (13C-fil) TOCSY	1 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA	100% D2O	150	5.7	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	700
3	Bruker	AVANCE	800
4	Bruker	AVANCE	900

NMR Refinement
Method	Details	Software
torsion angle dynamics, simulated annealing, molecular dynamics	Protein structure calculation was performed with CYANA 2.1, The 20 lowest-energy CT-Ler conformers were further energy-refined in explicit solvent using using CNS, DNA (LeeH) was defined as B-DNA followed by MD water refinement, including NMR restraints. The 20 lowest-energy protein structures were selected and docked onto LeeH using intermolecular NOEs and AIRs, Final scoring against experimental NMR and SAXS data. Packing, Ramachandran apprearance. Refinement against Small-Angle X-ray Scattering (SAXS) data, Quality assessment.	NMRPipe

NMR Ensemble Information
Conformer Selection Criteria	target function
Conformers Calculated Total Number	400
Conformers Submitted Total Number	20
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	NMRPipe		Delaglio, Zhengrong and Bax
2	nmr spectra acquisition	TopSpin		Bruker Biospin
3	structure calculation	CYANA		Guntert, Mumenthaler and Wuthrich
4	energy water refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
5	chemical shift assignment	CARA		Keller and Wuthrich
6	prediction of protein phi and psi angles using a chemical shift database	TALOS		Cornilescu, Delaglio and Bax
7	fitting to experimental scattering curves	CRYSOL		Svergun D.I., Barberato C. and Koch M.H.J.
8	data-driven docking using cns as structure calculation engine	HADDOCK		Alexandre Bonvin
9	molecular dynamics refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
10	quality assessment	Procheck		Laskowski and MacArthur
11	refinement	CYANA		Guntert, Mumenthaler and Wuthrich
12	refinement	CNS		Brunger, Adams, Clore, Gros, Nilges and Read
13	refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
14	refinement	HADDOCK		Alexandre Bonvin
15	refinement	CRYSOL		Svergun D.I., Barberato C. and Koch M.H.J.
16	refinement	Procheck		Laskowski and MacArthur

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.