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

©Jiří Černý & Bohdan Schneider

Arrested RNA Polymerase II reactivation intermediate

Results of the assignment of 22 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
013po3_N_DG2_DG3NANNANT00.72BB11
023po3_N_DG3_DT4NANNANT00.60AA06
033po3_N_DT4_DA5A-BAB01570.29AB01
043po3_N_DA5_DA6BB2BB07100.40BB07
053po3_N_DA6_DG7B-ABA13370.28BA13
063po3_N_DG7_DC8NANNANT00.51AB04
073po3_P_C7_C8NANNANT01.38AA06
083po3_P_C8_C9NANNANT00.95BB07
093po3_P_C9_C10B-ABA0180.35BA01
103po3_P_C10_C11NANNANT00.59AB03
113po3_T_DG10_DC11NANNANT00.52BB11
123po3_T_DC11_DT12BBBBB00370.40BB00
133po3_T_DT12_DT13BBBBB00560.32BB00
143po3_T_DT13_DA14BBBBB00200.54BB00
153po3_T_DA14_DC15B-ABA08710.27BA08
163po3_T_DC15_DC16AAAAA00380.33AA00
173po3_T_DC16_DT17AAAAA09830.24AA09
183po3_T_DT17_DG18NANNANT00.79OP06
193po3_T_DG18_DG19AAAAA00830.17AA00
203po3_T_DG19_DT20AAAAA04440.35AA04
213po3_T_DT20_DG21AAAAA08610.32AA08
223po3_T_DG21_BRU22NANNANT00.67AA01

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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