DNATCO v3.2: results

Crystal structure of the Pepper aptamer in complex with HBC, cesium soak

Results of the assignment of 48 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	7eoj_A_GDP1_G2	AAA	AA00	56	0.11	AA00
02	7eoj_A_G2_C3	AAA	AA00	89	0.13	AA00
03	7eoj_A_C3_G4	AAA	AA00	90	0.19	AA00
04	7eoj_A_G4_C5	AAA	AA00	92	0.20	AA00
05	7eoj_A_C5_A6	A-B	AB05	12	0.74	AB05
06	7eoj_A_A6_C7	NAN	NANT	0	0.54	OP26
07	7eoj_A_C7_U8	AAA	AA04	36	0.56	AA04
08	7eoj_A_U8_G9	NAN	NANT	0	0.64	AB05
09	7eoj_A_G9_G10	NAN	NANT	0	0.60	OP15
10	7eoj_A_G10_C11	AAA	AA00	76	0.24	AA00
11	7eoj_A_C11_G12	AAA	AA00	82	0.18	AA00
12	7eoj_A_G12_C13	AAA	AA00	95	0.17	AA00
13	7eoj_A_C13_U14	AAA	AA00	93	0.14	AA00
14	7eoj_A_U14_G15	NAN	NANT	0	0.51	AA06
15	7eoj_A_G15_C16	AAw	AA01	40	0.28	AA01
16	7eoj_A_C16_G17	AAw	AA11	86	0.28	AA11
17	7eoj_A_G17_C18	NAN	NANT	0	0.65	AA01
18	7eoj_A_C18_C19	AAw	AA01	70	0.20	AA01
19	7eoj_A_C19_U20	AAA	AA08	46	0.61	AA08
20	7eoj_A_U20_U21	NAN	NANT	0	0.89	OP09
21	7eoj_A_U21_C22	NAN	NANT	0	0.56	OP20
22	7eoj_A_C22_G23	NAN	NANT	0	0.98	BA17
23	7eoj_A_G23_G24	NAN	NANT	0	1.17	BA10
24	7eoj_A_G24_G25	NAN	NANT	0	0.60	AA01
25	7eoj_A_G25_C26	NAN	NANT	0	0.72	AB02
26	7eoj_A_C26_G27	AAA	AA08	70	0.26	AA08
27	7eoj_A_G27_C28	AAA	AA00	91	0.22	AA00
28	7eoj_A_C28_C29	OPN	OP06	26	0.67	OP06
29	7eoj_A_C29_A30	AAA	AA00	67	0.31	AA00
30	7eoj_A_A30_A31	AAA	AA00	62	0.35	AA00
31	7eoj_A_A31_U32	AAA	AA00	84	0.26	AA00
32	7eoj_A_U32_C33	NAN	NANT	0	1.05	IC07
33	7eoj_A_C33_G34	AAA	AA08	32	0.57	AA08
34	7eoj_A_G34_U35	AAA	AA00	81	0.28	AA00
35	7eoj_A_U35_A36	OPN	OP04	91	0.17	OP04
36	7eoj_A_A36_G37	AAA	AA00	69	0.25	AA00
37	7eoj_A_G37_C38	AAA	AA00	90	0.12	AA00
38	7eoj_A_C38_G39	AAA	AA00	86	0.19	AA00
39	7eoj_A_G39_U40	AAA	AA00	84	0.24	AA00
40	7eoj_A_U40_G41	ICL	IC04	48	0.38	IC04
41	7eoj_A_G41_U42	NAN	NANT	0	0.67	OP22
42	7eoj_A_U42_C43	NAN	NANT	0	0.64	OP26
43	7eoj_A_C43_G44	AAw	AA05	59	0.33	AA05
44	7eoj_A_G44_G45	AAA	AA00	52	0.32	AA00
45	7eoj_A_G45_C46	AAA	AA00	91	0.14	AA00
46	7eoj_A_C46_G47	AAA	AA00	88	0.10	AA00
47	7eoj_A_G47_C48	AAA	AA00	92	0.13	AA00
48	7eoj_A_C48_C49	AAA	AA00	90	0.22	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

Show

Color by conformation group (pyramids)

Color by conformation group (pyramids)

group
visible

Color by NtC (balls)

Color by NtC (balls)

A-B

B-A

B

IC

OPN

Z

N

Click the Summary/Torsions/Similar/... tabs for more details.
Center view on step or molecule.
Show reference and contacts	model altloc