Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
The Crystal Structure of an RNA/DNA Hybrid Reveals Novel Intermolecular Intercalation
Click a row in table or a step in viewer for analysis of results. Click column headers to sort data.
Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
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.
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 number | Step name | CANA | NtC | confal | rmsd |
|---|---|---|---|---|---|
| 01 | 1jb8_A_C1_A2 | ICL | IC01 | 18 | 0.37 |
| 02 | 1jb8_A_A2_A3 | B-A | BA13 | 72 | 0.31 |
| 03 | 1jb8_A_A3_A4 | AAA | AA00 | 86 | 0.18 |
| 04 | 1jb8_A_A4_G5 | AAA | AA04 | 42 | 0.50 |
| 05 | 1jb8_A_G5_A6 | AAA | AA00 | 82 | 0.21 |
| 06 | 1jb8_A_A6_A7 | AAA | AA00 | 94 | 0.19 |
| 07 | 1jb8_A_A7_A8 | AAA | AA00 | 92 | 0.21 |
| 08 | 1jb8_A_A8_A9 | AAA | AA00 | 95 | 0.12 |
| 09 | 1jb8_A_A9_G10 | AAA | AA00 | 73 | 0.14 |
| 10 | 1jb8_B_DC11_DT12 | AAA | AA00 | 68 | 0.24 |
| 11 | 1jb8_B_DT12_DT13 | AAw | AA01 | 75 | 0.17 |
| 12 | 1jb8_B_DT13_DT14 | AAA | AA00 | 56 | 0.25 |
| 13 | 1jb8_B_DT14_DT15 | AAA | AA00 | 79 | 0.23 |
| 14 | 1jb8_B_DT15_DC16 | AAA | AA00 | 94 | 0.15 |
| 15 | 1jb8_B_DC16_DT17 | AAA | AA00 | 83 | 0.32 |
| 16 | 1jb8_B_DT17_DT18 | AAA | AA00 | 93 | 0.18 |
| 17 | 1jb8_B_DT18_DT19 | AAA | AA00 | 72 | 0.22 |
| 18 | 1jb8_B_DT19_DG20 | NAN | NANT | 0 | 0.53 |
Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
|
step: Table of conformers |
| δ1 | ε1 | ζ1 | α2 | β2 | γ2 | δ2 | χ1 | χ2 | μ | NN | CC | |
| step_torsions | ||||||||||||
| ntC_average | ||||||||||||
| Δ torsions | ||||||||||||
| torsion scores |
| comments | step 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).
Browse conformers
Show
| Color by conformation group (pyramids) | |
|---|---|
| group | |||||||||
| visible |
| Color by NtC (balls) |
|---|
| A | ||||
|---|---|---|---|---|
| A-B | ||||
|---|---|---|---|---|
| B-A | ||||
|---|---|---|---|---|
| B | ||||
|---|---|---|---|---|
| IC | ||||
|---|---|---|---|---|
| OPN | ||||
|---|---|---|---|---|
| Z | ||||
|---|---|---|---|---|
| N | ||||
|---|---|---|---|---|