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Conformers: ABBIImiBZICOPNSYNN
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Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

Results of the assignment of 60 detected steps in 10 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
017nbk-m10_A_DC1_DG2A-BAB01740.28 AB01
027nbk-m1_A_DC1_DG2A-BAB01870.19 AB01
037nbk-m2_A_DC1_DG2A-BAB01790.27 AB01
047nbk-m3_A_DC1_DG2A-BAB01830.23 AB01
057nbk-m4_A_DC1_DG2A-BAB01810.25 AB01
067nbk-m5_A_DC1_DG2A-BAB01870.21 AB01
077nbk-m6_A_DC1_DG2A-BAB01850.24 AB01
087nbk-m7_A_DC1_DG2A-BAB01800.25 AB01
097nbk-m8_A_DC1_DG2A-BAB01840.22 AB01
107nbk-m9_A_DC1_DG2A-BAB01810.24 AB01
117nbk-m10_A_DG2_DT3BBBBB00830.19 BB00
127nbk-m1_A_DG2_DT3BBBBB00760.23 BB00
137nbk-m2_A_DG2_DT3BBBBB00790.20 BB00
147nbk-m3_A_DG2_DT3BBBBB00830.20 BB00
157nbk-m4_A_DG2_DT3BBBBB00790.21 BB00
167nbk-m5_A_DG2_DT3BBBBB00860.16 BB00
177nbk-m6_A_DG2_DT3BBBBB00760.20 BB00
187nbk-m7_A_DG2_DT3BBBBB00750.20 BB00
197nbk-m8_A_DG2_DT3BBBBB00830.16 BB00
207nbk-m9_A_DG2_DT3BBBBB00800.18 BB00
217nbk-m10_A_DT3_DA4BBBBB00700.30 BB00
227nbk-m1_A_DT3_DA4BBBBB00630.39 BB00
237nbk-m2_A_DT3_DA4BBBBB00650.30 BB00
247nbk-m3_A_DT3_DA4BBBBB00670.30 BB00
257nbk-m4_A_DT3_DA4BBBBB00540.33 BB00
267nbk-m5_A_DT3_DA4BBBBB00640.37 BB00
277nbk-m6_A_DT3_DA4BBBBB00550.35 BB00
287nbk-m7_A_DT3_DA4BBBBB00600.31 BB00
297nbk-m8_A_DT3_DA4BBBBB00660.33 BB00
307nbk-m9_A_DT3_DA4BBBBB00660.30 BB00
317nbk-m10_B_DC7_DG8A-BAB05930.22 AB05
327nbk-m1_B_DC7_DG8A-BAB01710.28 AB01
337nbk-m2_B_DC7_DG8A-BAB01760.20 AB01
347nbk-m3_B_DC7_DG8A-BAB01820.23 AB01
357nbk-m4_B_DC7_DG8A-BAB01820.22 AB01
367nbk-m5_B_DC7_DG8A-BAB05910.20 AB05
377nbk-m6_B_DC7_DG8A-BAB05860.21 AB05
387nbk-m7_B_DC7_DG8A-BAB01810.24 AB01
397nbk-m8_B_DC7_DG8A-BAB01680.31 AB01
407nbk-m9_B_DC7_DG8A-BAB01840.18 AB01
417nbk-m10_B_DG8_DT9BBBBB00820.19 BB00
427nbk-m1_B_DG8_DT9BBBBB00710.27 BB00
437nbk-m2_B_DG8_DT9BBBBB00850.17 BB00
447nbk-m3_B_DG8_DT9BBBBB00790.18 BB00
457nbk-m4_B_DG8_DT9BBBBB00810.17 BB00
467nbk-m5_B_DG8_DT9BBBBB00620.32 BB00
477nbk-m6_B_DG8_DT9BBBBB00800.21 BB00
487nbk-m7_B_DG8_DT9BBBBB00800.18 BB00
497nbk-m8_B_DG8_DT9BBBBB00780.20 BB00
507nbk-m9_B_DG8_DT9BBBBB00840.16 BB00
517nbk-m10_B_DT9_DA10BBBBB00690.30 BB00
527nbk-m1_B_DT9_DA10BBBBB00520.36 BB00
537nbk-m2_B_DT9_DA10BBBBB00750.28 BB00
547nbk-m3_B_DT9_DA10BBBBB00680.31 BB00
557nbk-m4_B_DT9_DA10BBBBB00570.36 BB00
567nbk-m5_B_DT9_DA10BBBBB00650.32 BB00
577nbk-m6_B_DT9_DA10BBBBB00600.34 BB00
587nbk-m7_B_DT9_DA10BBBBB00660.30 BB00
597nbk-m8_B_DT9_DA10BBBBB00670.29 BB00
607nbk-m9_B_DT9_DA10BBBBB00690.31 BB00

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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