Thrombin-aptamer recognition: a revealed ambiguity” by I. Russo Krauss et al.
SUPPLEMENTARY MATERIAL

Space group	I222	
Cell parameters		
a (Å)	68.21	
b (Å)	110.57	
c (Å)	120.92	
α, β, γ (°)	90.00	
Refinement Results		
Resolution limits (Å) 	50.00-2.15	
Number of reflections used
 in the refinement (F>2σ(F))	23598	
No. of reflections in working set	22464	
No. of reflections in test set	1134	
Rworking/Rfree (%) 	0.196/0.252	
No. of protein atoms	2374	
No. of aptamer atoms	306	
No. of ligand atoms	44	
No. of water molecules	250	
No. of ions	2	
RMSD from ideal values		
Bond lengths (Å) 	0.02	
Bond angles (°)	2.11	
Dihedral angles (°)	26.33	
Improper angles (°)	1.67	
		
Average B-factors (Å2)		
Protein, overall 	18.29	
Main chains	17.03	
Side chains	19.52	
Ions, solvent and ligand atoms	28.49	
Aptamer atoms	25.90	
		
Ramachandran plot statistics		
Residues in the most favored regions (%)	86.3	
Residues in the additionally allowed  regions (%)	13.7	
Residues in the generously allowed  regions (%)	-	

Table S1 Summary of refinement statistics.

		RMSD from the least squares plane of the tetrads (Å)	Dihedral angles between the planes of the four guanine groups and the least squares plane of the tetrad (°)	Dihedral angle between the least squares planes of the two  tetrads (°)	Separation distance of the tetrads along the chain axis (Å)	
Crystallographic
structure	Tetrad 1	0.25	Gua1
2.3	Gua6
11.4	Gua10
11.3	Gua15
8.9	0.8	3.40	
	Tetrad 2	0.22	Gua2
8.0	Gua5
2.7	Gua11
10.6	Gua14
6.3			
Free structure in solution (21)	Tetrad 1	0.37	Gua1
14.7	Gua6
10.6	Gua10
10.3	Gua15
-17.1	1.5	3.70	
	Tetrad 2	0.38	Gua2
-8.0	Gua5
10.4	Gua11
-20.9	Gua14
11.6			

Table S2 Geometry of the mTBA core in the crystallographic structure and the free structure in solution (21).

A   B 

Figure S1 (A) Omit Fo-Fc electron density map (4.0 σ level) of the residues bound by the 5’-5’ linkage (Thy3 and Thy4). (B) Omit Fo-Fc electron density map (6.0 σ level) of the potassium ion inserted between mTBA quartets. The polarity inversion site is depicted in magenta. For sake of clarity the bases of loop residues are not shown 

Figure S2 Representation of the C8…H-O4’ interaction in mTBA.

Figure S3 Example of sequential N2-water-water-C8 hydrogen bonds found in the hydration network of mTBA. Omit Fo-Fc electron density map (4.0 σ level) of the hydrogen bonded residues and water molecules is also shown.

Figure S4 Cross-eye stereo view of the 77-79 β-turn of thrombin-mTBA complex (purple) superimposed to the unbound thrombin molecule (PDB code 1PPB) (cyan) (6), showing the flip of the central peptide.