Conformers:
ABBIImiBZICOPNSYNN
Click the Summary/Torsions/Similar/... tabs for more details.
Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms
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 55 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 | 2rdj_C_DG1_DG2 | BBB | BB00 | 74 | 0.18 |
| 02 | 2rdj_C_DG2_DG3 | B12 | BB04 | 76 | 0.19 |
| 03 | 2rdj_C_DG3_DA4 | NAN | NANT | 0 | 0.64 |
| 04 | 2rdj_C_DA4_DC5 | NAN | NANT | 0 | 0.73 |
| 05 | 2rdj_C_DC5_DC6 | BBB | BB01 | 12 | 0.50 |
| 06 | 2rdj_C_DC6_DC7 | BBB | BB01 | 58 | 0.21 |
| 07 | 2rdj_C_DC7_DT8 | BBB | BB01 | 40 | 0.27 |
| 08 | 2rdj_C_DT8_DT9 | BBB | BB00 | 48 | 0.23 |
| 09 | 2rdj_C_DT9_DC10 | BBB | BB00 | 91 | 0.18 |
| 10 | 2rdj_C_DC10_DG11 | BBB | BB01 | 81 | 0.24 |
| 11 | 2rdj_C_DG11_DA12 | BBB | BB01 | 85 | 0.25 |
| 12 | 2rdj_C_DA12_DA13 | NAN | NANT | 0 | 0.39 |
| 13 | 2rdj_C_DA13_DT14 | AAA | AA00 | 49 | 0.25 |
| 14 | 2rdj_D_DT3_DT4 | NAN | NANT | 0 | 0.80 |
| 15 | 2rdj_D_DT4_DA5 | BBB | BB00 | 92 | 0.10 |
| 16 | 2rdj_D_DA5_DT6 | BBB | BB01 | 81 | 0.17 |
| 17 | 2rdj_D_DT6_DT7 | BBB | BB01 | 70 | 0.26 |
| 18 | 2rdj_D_DT7_DC8 | BBB | BB01 | 59 | 0.21 |
| 19 | 2rdj_D_DC8_DG9 | BBB | BB00 | 11 | 0.23 |
| 20 | 2rdj_D_DG9_DA10 | B12 | BB04 | 21 | 0.27 |
| 21 | 2rdj_D_DA10_DA11 | BBB | BB00 | 86 | 0.30 |
| 22 | 2rdj_D_DA11_DG12 | NAN | NANT | 0 | 0.57 |
| 23 | 2rdj_D_DG12_DG13 | B-A | BA08 | 61 | 0.29 |
| 24 | 2rdj_D_DG13_DG14 | AAA | AA00 | 52 | 0.31 |
| 25 | 2rdj_D_DG14_DT15 | A-B | AB01 | 21 | 0.30 |
| 26 | 2rdj_D_DT15_DC16 | NAN | NANT | 0 | 0.33 |
| 27 | 2rdj_D_DC16_DC17 | NAN | NANT | 0 | 0.49 |
| 28 | 2rdj_D_DC17_DC18 | NAN | NANT | 0 | 0.46 |
| 29 | 2rdj_E_DG1_DG2 | BBB | BB00 | 77 | 0.23 |
| 30 | 2rdj_E_DG2_DG3 | B12 | BB04 | 65 | 0.26 |
| 31 | 2rdj_E_DG3_DA4 | BBB | BB00 | 91 | 0.12 |
| 32 | 2rdj_E_DA4_DC5 | BBB | BB01 | 85 | 0.19 |
| 33 | 2rdj_E_DC5_DC6 | BBB | BB00 | 60 | 0.31 |
| 34 | 2rdj_E_DC6_DC7 | BBB | BB01 | 76 | 0.24 |
| 35 | 2rdj_E_DC7_DT8 | BBB | BB00 | 79 | 0.23 |
| 36 | 2rdj_E_DT8_DT9 | BBB | BB00 | 93 | 0.12 |
| 37 | 2rdj_E_DT9_DC10 | BBB | BB00 | 23 | 0.28 |
| 38 | 2rdj_E_DC10_DG11 | BBB | BB01 | 83 | 0.24 |
| 39 | 2rdj_E_DG11_DA12 | B-A | BA01 | 8 | 0.35 |
| 40 | 2rdj_E_DA12_DA13 | AAA | AA00 | 47 | 0.24 |
| 41 | 2rdj_E_DA13_DT14 | AAA | AA08 | 52 | 0.24 |
| 42 | 2rdj_F_DT4_DA5 | NAN | NANT | 0 | 0.51 |
| 43 | 2rdj_F_DA5_DT6 | B-A | BA05 | 89 | 0.17 |
| 44 | 2rdj_F_DT6_DT7 | AAA | AA02 | 49 | 0.62 |
| 45 | 2rdj_F_DT7_DC8 | A-B | AB01 | 25 | 0.46 |
| 46 | 2rdj_F_DC8_DG9 | B12 | BB04 | 68 | 0.24 |
| 47 | 2rdj_F_DG9_DA10 | BBB | BB00 | 88 | 0.13 |
| 48 | 2rdj_F_DA10_DA11 | B12 | BB04 | 71 | 0.15 |
| 49 | 2rdj_F_DA11_DG12 | BBB | BB00 | 97 | 0.20 |
| 50 | 2rdj_F_DG12_DG13 | miB | BB10 | 47 | 0.33 |
| 51 | 2rdj_F_DG13_DG14 | BBB | BB01 | 34 | 0.23 |
| 52 | 2rdj_F_DG14_DT15 | A-B | AB03 | 69 | 0.42 |
| 53 | 2rdj_F_DT15_DC16 | BBB | BB00 | 53 | 0.23 |
| 54 | 2rdj_F_DC16_DC17 | BBB | BB01 | 50 | 0.30 |
| 55 | 2rdj_F_DC17_DC18 | AAA | AA02 | 35 | 0.49 |
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
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