Conformers:
ABBIImiBZICOPNSYNN
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CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: THE HAMMERHEAD RIBOZYME
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 39 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 | 299d_A_U21_C30 | AAA | AA00 | 32 | 0.32 |
| 02 | 299d_A_G22_U21 | AAA | AA00 | 27 | 0.28 |
| 03 | 299d_A_G23_G22 | NAN | NANT | 0 | 0.56 |
| 04 | 299d_A_U24_G23 | AAA | AA00 | 91 | 0.13 |
| 05 | 299d_A_G25_U24 | AAA | AA08 | 59 | 0.35 |
| 06 | 299d_A_C30_U40 | AAA | AA02 | 13 | 0.45 |
| 07 | 299d_A_U40_G50 | OPN | OP04 | 20 | 0.12 |
| 08 | 299d_A_G50_A60 | AAA | AA00 | 41 | 0.41 |
| 09 | 299d_A_A60_U70 | OPN | OP01 | 36 | 0.33 |
| 10 | 299d_A_U70_G80 | NAN | NANT | 0 | 0.35 |
| 11 | 299d_A_G80_A90 | NAN | NANT | 0 | 1.43 |
| 12 | 299d_A_A90_G101 | NAN | NANT | 0 | 1.05 |
| 13 | 299d_A_G101_G102 | AAw | AA01 | 35 | 0.35 |
| 14 | 299d_A_G102_C103 | AAA | AA00 | 64 | 0.19 |
| 15 | 299d_A_C103_C104 | AAA | AA00 | 86 | 0.23 |
| 16 | 299d_B_A11_C12 | NAN | NANT | 0 | 0.34 |
| 17 | 299d_B_C12_C13 | AAA | AA00 | 10 | 0.40 |
| 18 | 299d_B_C13_A14 | AAA | AA00 | 61 | 0.26 |
| 19 | 299d_B_A14_C15 | AAA | AA00 | 52 | 0.20 |
| 20 | 299d_B_G31.L_U32.L | NAN | NANT | 0 | 0.33 |
| 21 | 299d_B_U32.L_A33.L | AAA | AA08 | 36 | 0.38 |
| 22 | 299d_B_A33.L_A34.L | AAA | AA00 | 23 | 0.26 |
| 23 | 299d_B_A34.L_G164 | NAN | NANT | 0 | 1.08 |
| 24 | 299d_B_C111_G120 | AAA | AA00 | 47 | 0.42 |
| 25 | 299d_B_C112_C111 | AAA | AA00 | 60 | 0.23 |
| 26 | 299d_B_G113_C112 | AAA | AA00 | 79 | 0.13 |
| 27 | 299d_B_G114_G113 | AAA | AA00 | 85 | 0.10 |
| 28 | 299d_B_G120_A130 | AAu | AA12 | 63 | 0.49 |
| 29 | 299d_B_A130_A140 | AAA | AA00 | 24 | 0.46 |
| 30 | 299d_B_A140_A151 | AAA | AA00 | 83 | 0.26 |
| 31 | 299d_B_A151_C152 | AAA | AA08 | 58 | 0.36 |
| 32 | 299d_B_C152_U153 | AAA | AA00 | 79 | 0.16 |
| 33 | 299d_B_U153_C154 | AAA | AA00 | 70 | 0.23 |
| 34 | 299d_B_C154_G31.L | AAA | AA00 | 61 | 0.34 |
| 35 | 299d_B_U161_C170 | AAu | AA13 | 6 | 0.83 |
| 36 | 299d_B_G162_U161 | AAA | AA03 | 40 | 0.41 |
| 37 | 299d_B_A163_G162 | AAA | AA00 | 83 | 0.20 |
| 38 | 299d_B_G164_A163 | AAA | AA00 | 73 | 0.17 |
| 39 | 299d_B_C170_A11 | AAA | AA00 | 23 | 0.28 |
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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