Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP
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 37 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 | 4yfu_B_DC21_DA22 | BBB | BB00 | 54 | 0.34 |
| 02 | 4yfu_B_DA22_DT23 | BBB | BB01 | 77 | 0.19 |
| 03 | 4yfu_B_DT23_DG24 | BBB | BB00 | 30 | 0.26 |
| 04 | 4yfu_B_DG24_DA25 | B-A | BA08 | 37 | 0.29 |
| 05 | 4yfu_B_DA25_DT26 | AAA | AA00 | 37 | 0.20 |
| 06 | 4yfu_B_DT26_DG27 | AAA | AA00 | 41 | 0.21 |
| 07 | 4yfu_B_DG27_DC28 | AAA | AA00 | 89 | 0.19 |
| 08 | 4yfu_C_DC4_DG5 | NAN | NANT | 0 | 1.28 |
| 09 | 4yfu_C_DG5_DA6 | NAN | NANT | 0 | 0.41 |
| 10 | 4yfu_C_DA6_DG7 | AAA | AA00 | 76 | 0.19 |
| 11 | 4yfu_C_DG7_DC8 | AAw | AA01 | 91 | 0.15 |
| 12 | 4yfu_C_DC8_DA9 | A-B | AB04 | 81 | 0.15 |
| 13 | 4yfu_C_DA9_DT10 | B-A | BA05 | 80 | 0.23 |
| 14 | 4yfu_C_DT10_DC11 | B-A | BA05 | 69 | 0.33 |
| 15 | 4yfu_C_DC11_DA12 | A-B | AB01 | 74 | 0.08 |
| 16 | 4yfu_C_DA12_DT13 | BBB | BB00 | 73 | 0.16 |
| 17 | 4yfu_C_DT13_DG14 | BBB | BB00 | 67 | 0.24 |
| 18 | 4yfu_E_DC21_DA22 | BBB | BB00 | 22 | 0.42 |
| 19 | 4yfu_E_DA22_DT23 | BBB | BB01 | 86 | 0.15 |
| 20 | 4yfu_E_DT23_DG24 | BBB | BB00 | 34 | 0.24 |
| 21 | 4yfu_E_DG24_DA25 | B-A | BA08 | 48 | 0.32 |
| 22 | 4yfu_E_DA25_DT26 | NAN | NANT | 0 | 0.31 |
| 23 | 4yfu_E_DT26_DG27 | NAN | NANT | 0 | 0.23 |
| 24 | 4yfu_E_DG27_DC28 | AAA | AA00 | 91 | 0.20 |
| 25 | 4yfu_F_DG1_DA2 | NAN | NANT | 0 | 0.61 |
| 26 | 4yfu_F_DA2_DG3 | BBB | BB00 | 31 | 0.60 |
| 27 | 4yfu_F_DG3_DC4 | NAN | NANT | 0 | 0.51 |
| 28 | 4yfu_F_DC4_DG5 | NAN | NANT | 0 | 1.37 |
| 29 | 4yfu_F_DG5_DA6 | OPN | OP10 | 26 | 0.47 |
| 30 | 4yfu_F_DA6_DG7 | AAA | AA00 | 83 | 0.19 |
| 31 | 4yfu_F_DG7_DC8 | AAw | AA01 | 90 | 0.15 |
| 32 | 4yfu_F_DC8_DA9 | A-B | AB04 | 85 | 0.14 |
| 33 | 4yfu_F_DA9_DT10 | BBB | BB01 | 85 | 0.17 |
| 34 | 4yfu_F_DT10_DC11 | B-A | BA05 | 85 | 0.28 |
| 35 | 4yfu_F_DC11_DA12 | A-B | AB03 | 82 | 0.33 |
| 36 | 4yfu_F_DA12_DT13 | BBB | BB01 | 87 | 0.16 |
| 37 | 4yfu_F_DT13_DG14 | BBB | BB00 | 62 | 0.18 |
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 | ||||
|---|---|---|---|---|