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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

RNA Polymerase II initial transcribing complex with a 4nt DNA-RNA hybrid

Results of the assignment of 17 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
014a3b_N_DA2_DA3NANNANT00.37BA10
024a3b_N_DA3_DG4BBwBB16670.50BB16
034a3b_N_DG4_DT5NANNANT00.61BA08
044a3b_P_A7_G8AAwAA01450.28AA01
054a3b_P_G8_G9AAwAA1080.49AA10
064a3b_P_G9_A10AAAAA08510.27AA08
074a3b_T_DA13_DC14BBBBB01400.44BB01
084a3b_T_DC14_DT15NANNANT00.52BA08
094a3b_T_DT15_DT16A-BAB03480.51AB03
104a3b_T_DT16_DT17B-ABA08390.46BA08
114a3b_T_DT17_DT18AAAAA00590.38AA00
124a3b_T_DT18_DT19NANNANT01.53OP05
134a3b_T_DT19_DC20AAAAA00860.14AA00
144a3b_T_DC20_DC21AAwAA01550.20AA01
154a3b_T_DC21_BRU22NANNANT00.60IC04
164a3b_T_BRU22_DG23NANNANT00.49BB16
174a3b_T_DG23_DG24NANNANT00.46BB03

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

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).

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