Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Refinement of P4 stemloop structure using residual dipolar coupling data
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 26 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 | 2cd1_A_G1_G2 | NAN | NANT | 0 | 0.48 |
| 02 | 2cd1_A_G2_A3 | AAA | AA00 | 61 | 0.19 |
| 03 | 2cd1_A_A3_A4 | AAA | AA00 | 49 | 0.35 |
| 04 | 2cd1_A_A4_G5 | NAN | NANT | 0 | 0.29 |
| 05 | 2cd1_A_G5_U6 | NAN | NANT | 0 | 1.29 |
| 06 | 2cd1_A_U6_C7 | NAN | NANT | 0 | 0.99 |
| 07 | 2cd1_A_C7_C8 | AAA | AA00 | 24 | 0.33 |
| 08 | 2cd1_A_C8_G9 | AAA | AA00 | 72 | 0.17 |
| 09 | 2cd1_A_G9_G10 | AAA | AA00 | 65 | 0.18 |
| 10 | 2cd1_A_G10_U11 | AAA | AA00 | 54 | 0.28 |
| 11 | 2cd1_A_U11_C12 | NAN | NANT | 0 | 0.58 |
| 12 | 2cd1_A_C12_U13 | AAA | AA04 | 41 | 0.67 |
| 13 | 2cd1_A_U13_U14 | NAN | NANT | 0 | 2.53 |
| 14 | 2cd1_A_U14_C15 | NAN | NANT | 0 | 1.24 |
| 15 | 2cd1_A_C15_G16 | NAN | NANT | 0 | 1.05 |
| 16 | 2cd1_A_G16_G17 | NAN | NANT | 0 | 0.52 |
| 17 | 2cd1_A_G17_A18 | AAA | AA00 | 35 | 0.33 |
| 18 | 2cd1_A_A18_C19 | AAA | AA00 | 55 | 0.28 |
| 19 | 2cd1_A_C19_C20 | AAA | AA04 | 69 | 0.24 |
| 20 | 2cd1_A_C20_G21 | AAA | AA08 | 47 | 0.31 |
| 21 | 2cd1_A_G21_G22 | AAA | AA08 | 36 | 0.32 |
| 22 | 2cd1_A_G22_C23 | AAA | AA08 | 24 | 0.32 |
| 23 | 2cd1_A_C23_U24 | AAA | AA00 | 51 | 0.26 |
| 24 | 2cd1_A_U24_U25 | AAA | AA00 | 55 | 0.27 |
| 25 | 2cd1_A_U25_C26 | AAA | AA00 | 80 | 0.20 |
| 26 | 2cd1_A_C26_C27 | AAA | AA00 | 12 | 0.55 |
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 | ||||
|---|---|---|---|---|