DNATCO v3.2: results

Crystal structures of artificially designed homomeric RNA nanoarchitectures

Results of the assignment of 50 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.

step number	Step name	CANA	NtC	confal	rmsd
01	7jrr_A_GTP1_G2	NAN	NANT	0	0.49	AA04
02	7jrr_A_G2_A3	AAA	AA00	86	0.14	AA00
03	7jrr_A_A3_C4	AAA	AA00	58	0.16	AA00
04	7jrr_A_C4_G5	AAw	AA01	85	0.12	AA01
05	7jrr_A_G5_G6	AAA	AA00	19	0.50	AA00
06	7jrr_A_G6_G7	A-B	AB05	79	0.20	AB05
07	7jrr_A_G7_A8	NAN	NANT	0	0.80	BB07
08	7jrr_A_A8_G9	OPN	OP24	92	0.13	OP24
09	7jrr_A_G9_C10	AAA	AA00	81	0.19	AA00
10	7jrr_A_C10_U11	AAA	AA00	67	0.15	AA00
11	7jrr_A_U11_G12	AAA	AA00	70	0.14	AA00
12	7jrr_A_G12_A13	OPN	OP05	59	0.47	OP05
13	7jrr_A_A13_A14	AAA	AA00	19	0.36	AA00
14	7jrr_A_A14_C15	AAA	AA00	35	0.21	AA00
15	7jrr_A_C15_C16	AAA	AA00	41	0.33	AA00
16	7jrr_A_C16_A17	AAA	AA00	76	0.29	AA00
17	7jrr_A_A17_U18	AAA	AA00	81	0.22	AA00
18	7jrr_A_U18_C19	AAw	AA10	68	0.26	AA10
19	7jrr_A_C19_C20	AAA	AA00	74	0.26	AA00
20	7jrr_A_C20_A21	AAA	AA00	86	0.13	AA00
21	7jrr_A_A21_G22	AAA	AA00	83	0.13	AA00
22	7jrr_A_G22_C23	AAA	AA00	79	0.23	AA00
23	7jrr_A_C23_G24	AAA	AA00	77	0.22	AA00
24	7jrr_A_G24_A25	NAN	NANT	0	1.18	BB2S
25	7jrr_A_A25_A26	NAN	NANT	0	0.41	OP21
26	7jrr_A_A26_G27	NAN	NANT	0	0.53	OP20
27	7jrr_A_G27_A28	OPN	OP10	70	0.24	OP10
28	7jrr_A_A28_A29	AAw	AA01	90	0.16	AA01
29	7jrr_A_A29_C30	AAA	AA08	41	0.57	AA08
30	7jrr_A_C30_G31	AAA	AA00	83	0.15	AA00
31	7jrr_A_G31_U32	AAA	AA00	86	0.12	AA00
32	7jrr_A_U32_C33	AAA	AA00	94	0.14	AA00
33	7jrr_A_C33_C34	AAA	AA00	86	0.16	AA00
34	7jrr_A_C34_C35	AAA	AA00	54	0.29	AA00
35	7jrr_A_C35_G36	AAA	AA00	71	0.16	AA00
36	7jrr_A_G36_A37	AAA	AA00	92	0.10	AA00
37	7jrr_A_A37_C38	AAA	AA00	95	0.14	AA00
38	7jrr_A_C38_G39	AAA	AA00	38	0.23	AA00
39	7jrr_A_G39_G40	NAN	NANT	0	1.52	OP06
40	7jrr_A_G40_A41	AAA	AA00	23	0.35	AA00
41	7jrr_A_A41_U42	AAA	AA00	62	0.24	AA00
42	7jrr_A_U42_G43	AAA	AA00	53	0.18	AA00
43	7jrr_A_G43_G44	AAA	AA00	64	0.21	AA00
44	7jrr_A_G44_U45	AAA	AA08	81	0.34	AA08
45	7jrr_A_U45_U46	AAA	AA00	79	0.25	AA00
46	7jrr_A_U46_C47	AAA	AA00	86	0.21	AA00
47	7jrr_A_C47_G48	AAA	AA00	88	0.11	AA00
48	7jrr_A_G48_U49	AAA	AA00	81	0.12	AA00
49	7jrr_A_U49_C50	AAA	AA08	85	0.19	AA08
50	7jrr_A_C50_G51	AAA	AA00	46	0.28	AA00

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.

step:
Table of conformers

δ1

ε1

ζ1

α2

β2

γ2

δ2

χ1

χ2

μ

NN

CC

step_torsions

ntC_average

Δ torsions

torsion scores

comments step confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of conformers.

Download the papers

Description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
Definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
Example of application:
Schneider et al., Genes, 8(10), 278, (2017).

Browse conformers

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Color by conformation group (pyramids)

Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

Color by NtC (balls)

A

A-B

B-A

B

IC

OPN

Z

N

Click the Summary/Torsions/Similar/... tabs for more details.
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