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

©Jiří Černý & Bohdan Schneider

Crystal Structure Analysis Of A 2-O-[2-(methoxy)ethyl]-2-thiothymidine Modified Oligodeoxynucleotide Duplex

Results of the assignment of 18 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
012axb_A_DG1_DC2AAAAA08420.32AA08
022axb_A_DC2_DG3AAwAA01770.17AA01
032axb_A_DG3_DT4NANNANT00.55AA04
042axb_A_DT4_DA5AAwAA01530.25AA01
052axb_A_DA5_S2M6AAAAA04780.25AA04
062axb_A_S2M6_DA7AAAAA00580.32AA00
072axb_A_DA7_DC8AAAAA00710.19AA00
082axb_A_DC8_DG9AAAAA00540.16AA00
092axb_A_DG9_DC10AAAAA00520.31AA00
102axb_B_DG11_DC12NANNANT00.50BA01
112axb_B_DC12_DG13AAwAA10430.26AA10
122axb_B_DG13_DT14AAAAA00510.28AA00
132axb_B_DT14_DA15AAAAA00730.18AA00
142axb_B_DA15_S2M16AAAAA00810.17AA00
152axb_B_S2M16_DA17AAAAA00770.10AA00
162axb_B_DA17_DC18AAAAA00630.22AA00
172axb_B_DC18_DG19AAAAA00870.21AA00
182axb_B_DG19_DC20AAAAA00260.24AA00

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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