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Conformers: ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Solution structure of DNA:RNA hybrid containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification

Results of the assignment of 120 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
0017nbl-m10_A_DC1_DT2NANNANT00.83 BB16
0027nbl-m1_A_DC1_DT2BBBBB00240.54 BB00
0037nbl-m2_A_DC1_DT2NANNANT00.81 BB16
0047nbl-m3_A_DC1_DT2BBBBB00260.54 BB00
0057nbl-m4_A_DC1_DT2BBBBB00260.56 BB00
0067nbl-m5_A_DC1_DT2NANNANT00.85 BB16
0077nbl-m6_A_DC1_DT2BBBBB00120.58 BB00
0087nbl-m7_A_DC1_DT2BBBBB00220.51 BB00
0097nbl-m8_A_DC1_DT2BBBBB00320.55 BB00
0107nbl-m9_A_DC1_DT2BBBBB00250.57 BB00
0117nbl-m10_A_DT2_DA3BBBBB00480.38 BB00
0127nbl-m1_A_DT2_DA3BBBBB00490.35 BB00
0137nbl-m2_A_DT2_DA3BBBBB00310.51 BB00
0147nbl-m3_A_DT2_DA3BBBBB00510.34 BB00
0157nbl-m4_A_DT2_DA3BBBBB00460.40 BB00
0167nbl-m5_A_DT2_DA3BBBBB00620.36 BB00
0177nbl-m6_A_DT2_DA3BBBBB00380.41 BB00
0187nbl-m7_A_DT2_DA3BBBBB00470.40 BB00
0197nbl-m8_A_DT2_DA3BBBBB00450.33 BB00
0207nbl-m9_A_DT2_DA3BBBBB00630.29 BB00
0217nbl-m10_A_DA5_DC6B-ABA05610.30 BA05
0227nbl-m1_A_DA5_DC6BBBBB01710.25 BB01
0237nbl-m2_A_DA5_DC6BBBBB00750.22 BB00
0247nbl-m3_A_DA5_DC6BBBBB01730.22 BB01
0257nbl-m4_A_DA5_DC6B-ABA05320.31 BA05
0267nbl-m5_A_DA5_DC6B-ABA05780.28 BA05
0277nbl-m6_A_DA5_DC6BBBBB01580.27 BB01
0287nbl-m7_A_DA5_DC6BBBBB01680.24 BB01
0297nbl-m8_A_DA5_DC6B-ABA05480.20 BA05
0307nbl-m9_A_DA5_DC6B-ABA05730.34 BA05
0317nbl-m10_A_DC6_DG7BBBBB00150.34 BB00
0327nbl-m1_A_DC6_DG7B12BB04340.34 BB04
0337nbl-m2_A_DC6_DG7B12BB04100.51 BB04
0347nbl-m3_A_DC6_DG7BBwBB03270.42 BB03
0357nbl-m4_A_DC6_DG7BBBBB01290.30 BB01
0367nbl-m5_A_DC6_DG7BBBBB00440.33 BB00
0377nbl-m6_A_DC6_DG7BBBBB00590.31 BB00
0387nbl-m7_A_DC6_DG7BBBBB00220.29 BB00
0397nbl-m8_A_DC6_DG7BBBBB01120.29 BB01
0407nbl-m9_A_DC6_DG7BBBBB00140.30 BB00
0417nbl-m10_A_DG7_DG8BBBBB00780.27 BB00
0427nbl-m1_A_DG7_DG8BBBBB00680.31 BB00
0437nbl-m2_A_DG7_DG8BBBBB01670.22 BB01
0447nbl-m3_A_DG7_DG8BBBBB00610.35 BB00
0457nbl-m4_A_DG7_DG8BBBBB00780.24 BB00
0467nbl-m5_A_DG7_DG8BBBBB00760.27 BB00
0477nbl-m6_A_DG7_DG8BBBBB00790.27 BB00
0487nbl-m7_A_DG7_DG8BBBBB00730.31 BB00
0497nbl-m8_A_DG7_DG8BBBBB00760.30 BB00
0507nbl-m9_A_DG7_DG8BBBBB00650.37 BB00
0517nbl-m10_B_C9_C10AAAAA00770.15 AA00
0527nbl-m1_B_C9_C10AAAAA00920.15 AA00
0537nbl-m2_B_C9_C10AAAAA00470.19 AA00
0547nbl-m3_B_C9_C10AAAAA00490.22 AA00
0557nbl-m4_B_C9_C10AAAAA04780.31 AA04
0567nbl-m5_B_C9_C10AAAAA00410.21 AA00
0577nbl-m6_B_C9_C10AAAAA04810.23 AA04
0587nbl-m7_B_C9_C10AAAAA00700.20 AA00
0597nbl-m8_B_C9_C10AAAAA00810.16 AA00
0607nbl-m9_B_C9_C10AAAAA00760.27 AA00
0617nbl-m10_B_C10_G11AAAAA00830.14 AA00
0627nbl-m1_B_C10_G11AAAAA00790.21 AA00
0637nbl-m2_B_C10_G11AAAAA00690.24 AA00
0647nbl-m3_B_C10_G11AAAAA00780.18 AA00
0657nbl-m4_B_C10_G11AAAAA00740.14 AA00
0667nbl-m5_B_C10_G11AAAAA00680.21 AA00
0677nbl-m6_B_C10_G11AAAAA00830.14 AA00
0687nbl-m7_B_C10_G11AAAAA00750.15 AA00
0697nbl-m8_B_C10_G11AAAAA00680.16 AA00
0707nbl-m9_B_C10_G11AAAAA00280.21 AA00
0717nbl-m10_B_G11_U12AAAAA00830.16 AA00
0727nbl-m1_B_G11_U12AAAAA00450.20 AA00
0737nbl-m2_B_G11_U12AAAAA00650.23 AA00
0747nbl-m3_B_G11_U12AAAAA00720.16 AA00
0757nbl-m4_B_G11_U12AAAAA00630.16 AA00
0767nbl-m5_B_G11_U12AAAAA00820.13 AA00
0777nbl-m6_B_G11_U12AAAAA00860.19 AA00
0787nbl-m7_B_G11_U12AAAAA00740.15 AA00
0797nbl-m8_B_G11_U12AAAAA00730.15 AA00
0807nbl-m9_B_G11_U12AAAAA00720.18 AA00
0817nbl-m10_B_U12_G13AAAAA00460.17 AA00
0827nbl-m1_B_U12_G13AAAAA00730.16 AA00
0837nbl-m2_B_U12_G13AAAAA00660.18 AA00
0847nbl-m3_B_U12_G13AAAAA00580.21 AA00
0857nbl-m4_B_U12_G13AAAAA04660.26 AA04
0867nbl-m5_B_U12_G13AAAAA00790.16 AA00
0877nbl-m6_B_U12_G13AAAAA00680.21 AA00
0887nbl-m7_B_U12_G13AAAAA00230.25 AA00
0897nbl-m8_B_U12_G13AAAAA00610.18 AA00
0907nbl-m9_B_U12_G13AAAAA00560.20 AA00
0917nbl-m10_B_G13_U14AAAAA00680.16 AA00
0927nbl-m1_B_G13_U14AAAAA00830.15 AA00
0937nbl-m2_B_G13_U14AAAAA00590.26 AA00
0947nbl-m3_B_G13_U14AAAAA00620.20 AA00
0957nbl-m4_B_G13_U14AAAAA00780.16 AA00
0967nbl-m5_B_G13_U14AAAAA00660.23 AA00
0977nbl-m6_B_G13_U14AAAAA00480.28 AA00
0987nbl-m7_B_G13_U14AAAAA00550.18 AA00
0997nbl-m8_B_G13_U14AAAAA00780.18 AA00
1007nbl-m9_B_G13_U14AAAAA00580.18 AA00
1017nbl-m10_B_U14_A15AAAAA00340.24 AA00
1027nbl-m1_B_U14_A15AAAAA00230.22 AA00
1037nbl-m2_B_U14_A15AAAAA00270.27 AA00
1047nbl-m3_B_U14_A15AAAAA00160.23 AA00
1057nbl-m4_B_U14_A15AAAAA00280.23 AA00
1067nbl-m5_B_U14_A15AAAAA00270.23 AA00
1077nbl-m6_B_U14_A15AAAAA00420.24 AA00
1087nbl-m7_B_U14_A15AAAAA00460.22 AA00
1097nbl-m8_B_U14_A15AAAAA00800.16 AA00
1107nbl-m9_B_U14_A15AAAAA00470.20 AA00
1117nbl-m10_B_A15_G16AAuAA12240.23 AA12
1127nbl-m1_B_A15_G16AAuAA12140.24 AA12
1137nbl-m2_B_A15_G16AAuAA12190.23 AA12
1147nbl-m3_B_A15_G16AAAAA04250.53 AA04
1157nbl-m4_B_A15_G16AAuAA12170.24 AA12
1167nbl-m5_B_A15_G16AAuAA12160.24 AA12
1177nbl-m6_B_A15_G16AAuAA12330.22 AA12
1187nbl-m7_B_A15_G16AAuAA12380.24 AA12
1197nbl-m8_B_A15_G16AAAAA00350.41 AA00
1207nbl-m9_B_A15_G16AAAAA00410.37 AA00

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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