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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR SPECTRA

Results of the assignment of 24 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
01142d_A_DA1_DG2BBBBB01900.13BB01
02142d_A_DG2_DC3BBBBB01820.27BB01
03142d_A_DC3_DT4B-ABA05200.20BA05
04142d_A_DT4_DT5BBBBB01230.32BB01
05142d_A_DT5_DG6B-ABA05770.25BA05
06142d_A_DG6_DC7BBBBB00140.36BB00
07142d_A_DC7_DC8BBBBB01720.20BB01
08142d_A_DC8_DT9BBBBB01810.15BB01
09142d_A_DT9_DT10BBBBB01510.14BB01
10142d_A_DT10_DG11BBBBB01180.22BB01
11142d_A_DG11_DA12BBBBB00590.37BB00
12142d_A_DA12_DG13BBBBB00840.14BB00
13142d_B_DC14_DT15BBBBB00490.28BB00
14142d_B_DT15_DC16B-ABA05540.33BA05
15142d_B_DC16_DA17A-BAB01460.44AB01
16142d_B_DA17_DA18BBBBB00660.24BB00
17142d_B_DA18_DG19BBBBB00690.36BB00
18142d_B_DG19_DG20BBBBB01660.21BB01
19142d_B_DG20_DC21B-ABA05780.17BA05
20142d_B_DC21_DA22BBBBB01440.17BB01
21142d_B_DA22_DA23BBBBB01640.20BB01
22142d_B_DA23_DG24BBBBB00300.24BB00
23142d_B_DG24_DC25BBBBB01250.20BB01
24142d_B_DC25_DT26BBBBB01480.23BB01

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep 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).

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