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Conformers: ABBIImiBZICOPNSYNN
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Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli in complex with AP-site containing DNA substrate

Results of the assignment of 20 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 viewer for analysis of results. Click column headers to sort data.
Define restraints for steps within Å cartesian RMSD, global sigma scaling factor or use per step sigma scaling.
step numberStep nameCANANtCconfalrmsd
012ea0_B_DG401_DG402NANNANT00.58 BB04
022ea0_B_DG402_DC403NANNANT00.37 BB04
032ea0_B_DC403_DT404BBBBB00910.24 BB00
042ea0_B_DT404_DT405BBBBB00550.19 BB00
052ea0_B_DT405_DC406BBBBB01790.16 BB01
062ea0_B_DC406_DA407B-ABA05500.33 BA05
072ea0_B_DA407_DT408AAAAA02420.45 AA02
082ea0_B_DT408_DC409BBBBB01590.27 BB01
092ea0_B_DC409_DC410BBBBB01610.17 BB01
102ea0_B_DC410_DT411miBBB15250.48 BB15
112ea0_B_DT411_DG412NANNANT00.40 BB15
122ea0_C_DC422_DA423NANNANT00.50 BB07
132ea0_C_DA423_DG424NANNANT00.42 BB00
142ea0_C_DG424_DG425NANNANT00.20 BB04
152ea0_C_DG425_DA426B-ABA01230.35 BA01
162ea0_C_DG428_DA429NANNANT00.43 BA08
172ea0_C_DA429_DA430NANNANT00.36 AB02
182ea0_C_DA430_DG431NANNANT00.51 AB02
192ea0_C_DG431_DC432NANNANT00.43 BB03
202ea0_C_DC432_DC433NANNANT00.50 BB13

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.
Best NtC fitted to input structure.

Restraints

Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Restraints file for Phenix (steps with RMSD <= 0.5Å) [?]

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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