Conformers:
ABBIImiBZICOPNSYNN
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Crosslinked Hammerhead Ribozyme Initial State
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 38 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 | 1nyi_A_G11_U12 | AAA | AA08 | 42 | 0.27 |
| 02 | 1nyi_A_U12_G13 | AAA | AA00 | 92 | 0.14 |
| 03 | 1nyi_A_G13_G14 | AAw | AA06 | 61 | 0.32 |
| 04 | 1nyi_A_G14_U15 | AAA | AA03 | 83 | 0.28 |
| 05 | 1nyi_A_U15_C16 | AAA | AA00 | 58 | 0.25 |
| 06 | 1nyi_A_C16_U17 | AAA | AA00 | 84 | 0.14 |
| 07 | 1nyi_A_U17_G18 | OPN | OP04 | 48 | 0.18 |
| 08 | 1nyi_A_G18_A19 | AAA | AA00 | 25 | 0.41 |
| 09 | 1nyi_A_A19_U20 | OPN | OP01 | 75 | 0.42 |
| 10 | 1nyi_A_U20_G21 | NAN | NANT | 0 | 0.58 |
| 11 | 1nyi_A_G21_A22 | NAN | NANT | 0 | 1.27 |
| 12 | 1nyi_A_A22_G23 | AAw | AA05 | 49 | 0.25 |
| 13 | 1nyi_A_G23_G24 | AAA | AA08 | 65 | 0.21 |
| 14 | 1nyi_A_G24_C25 | AAA | AA08 | 80 | 0.21 |
| 15 | 1nyi_A_C25_C26 | AAA | AA00 | 78 | 0.21 |
| 16 | 1nyi_B_G102_C103 | AAA | AA00 | 62 | 0.20 |
| 17 | 1nyi_B_C103_C104 | AAA | AA00 | 51 | 0.16 |
| 18 | 1nyi_B_C104_G105 | AAA | AA08 | 61 | 0.44 |
| 19 | 1nyi_B_G105_A106 | NAN | NANT | 0 | 0.92 |
| 20 | 1nyi_B_A106_A107 | AAA | AA08 | 36 | 0.41 |
| 21 | 1nyi_B_A107_A108 | AAA | AA08 | 75 | 0.25 |
| 22 | 1nyi_B_A108_C109 | AAA | AA08 | 85 | 0.21 |
| 23 | 1nyi_B_C109_U110 | AAA | AA00 | 72 | 0.17 |
| 24 | 1nyi_B_U110_C111 | AAA | AA08 | 84 | 0.14 |
| 25 | 1nyi_B_C111_G112 | AAA | AA08 | 72 | 0.21 |
| 26 | 1nyi_B_G112_U113 | OPN | OP03 | 45 | 0.29 |
| 27 | 1nyi_B_U113_A114 | AAA | AA00 | 26 | 0.43 |
| 28 | 1nyi_B_A114_A115 | AAA | AA02 | 62 | 0.21 |
| 29 | 1nyi_B_A115_G116 | AAw | AA05 | 35 | 0.46 |
| 30 | 1nyi_B_G116_A117 | AAA | AA08 | 68 | 0.18 |
| 31 | 1nyi_B_A117_G118 | AAA | AA00 | 77 | 0.21 |
| 32 | 1nyi_B_G118_U119 | A-B | AB01 | 30 | 0.27 |
| 33 | 1nyi_B_U119_C120 | NAN | NANT | 0 | 0.94 |
| 34 | 1nyi_B_C120_A121 | AAA | AA04 | 57 | 0.23 |
| 35 | 1nyi_B_A121_C122 | AAw | AA01 | 79 | 0.21 |
| 36 | 1nyi_B_C122_C123 | AAA | AA00 | 65 | 0.26 |
| 37 | 1nyi_B_C123_A124 | AAA | AA00 | 67 | 0.21 |
| 38 | 1nyi_B_A124_C125 | AAA | AA00 | 78 | 0.19 |
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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| Color by conformation group (pyramids) | |
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| B | ||||
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