Table 1. Dataset of 24 RNA structures, twelve X-ray (six helical and six complex folded) and twelve NMR (six helical and six complex folded) structures, taken from the Protein Data Bank (PDB, http://www.rcsb.org/pdb/) (40). The fraction of single nucleotides (Nuc.) is calculated for each structure. Helical structures that have only base pairs have a fraction of 0.

Method/PDB id	Classification/system	Fraction unpaired	Nuc.	A	C	G	U	Mg2+	K+
X-ray	Helical
1D4R (41)	Single recognition particle RNA	0.04	54	8	18	22	6	4
1QC0 (42)	Plasmid copy control related RNA	0.00	38	6	13	13	6
2QEK (49)	HIV-1 dimerization initiation site	0.04	46	14	12	12	8	1	3
4K31 (43)	rRNA A-site	0.05	44	8	12	14	10
413D (44)	A-form RNA double helix	0.04	26	2	8	8	8
420D (50)	RNA with A(anti)-G(syn) mispairs	0.00	32	10	6	8	8
X-ray	Complex folded
4B5R (51)	SAM-I riboswitch	0.30	94	28	22	32	12
4FEJ (52)	Guanine riboswitch aptamer	0.31	67	16	17	17	17
4FRG (53)	Cobalamin riboswitch aptamer	0.34	84	27	19	22	16	7
4JF2 (54)	Class II preQ1 riboswitch	0.37	76	19	19	18	20	4
4KQY (55)	S-box (SAM-I) riboswitch	0.34	119	40	27	33	19	2
4P5J (56)	tRNA-like structure	0.36	83	17	28	22	16	2
NMR	Helical
1A4D (45)	Loop D/Loop E arm of 5S rRNA	0.07	41	6	10	17	8
2D18 (57)	HIV-1 dimerization initiation site	0.00	34	8	10	12	4
2KYD (58)	A-form RNA double helix	0.00	32	10	6	6	10
2L2J (48)	R/G stem loop RNA	0.10	42	7	13	13	9
2LPS (46)	ai5(gamma) group II intron	0.12	34	8	8	11	7
2LV0 (47)	Stem–loop from 23S rRNA	0.17	24	8	4	6	6
NMR	Complex folded
1YMO (59)	Telomerase RNA pseudoknot	0.36	47	13	13	9	12
2ADT (60)	Tetraloop–receptor complex	0.31	86	22	16	26	22
2LKR (61)	U2/U6 snRNA	0.37	111	29	22	25	35
2MHI (62)	CR4/5 domain of telomerase RNA	0.25	53	7	15	17	14
2MTK (63)	Ribozyme’s III-IV-V junction	0.36	47	7	13	16	11	6
2M8K (64)	Telomerase RNA pseudoknot	0.30	48	12	9	6	21
Total	Average		56	13	14	16	13