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

©Jiří Černý & Bohdan Schneider

Crystal structure of the Pepper aptamer in complex with HBC, cesium soak

Results of the assignment of 48 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
017eoj_A_GDP1_G2AAAAA00560.11AA00
027eoj_A_G2_C3AAAAA00890.13AA00
037eoj_A_C3_G4AAAAA00900.19AA00
047eoj_A_G4_C5AAAAA00920.20AA00
057eoj_A_C5_A6A-BAB05120.74AB05
067eoj_A_A6_C7NANNANT00.54OP26
077eoj_A_C7_U8AAAAA04360.56AA04
087eoj_A_U8_G9NANNANT00.64AB05
097eoj_A_G9_G10NANNANT00.60OP15
107eoj_A_G10_C11AAAAA00760.24AA00
117eoj_A_C11_G12AAAAA00820.18AA00
127eoj_A_G12_C13AAAAA00950.17AA00
137eoj_A_C13_U14AAAAA00930.14AA00
147eoj_A_U14_G15NANNANT00.51AA06
157eoj_A_G15_C16AAwAA01400.28AA01
167eoj_A_C16_G17AAwAA11860.28AA11
177eoj_A_G17_C18NANNANT00.65AA01
187eoj_A_C18_C19AAwAA01700.20AA01
197eoj_A_C19_U20AAAAA08460.61AA08
207eoj_A_U20_U21NANNANT00.89OP09
217eoj_A_U21_C22NANNANT00.56OP20
227eoj_A_C22_G23NANNANT00.98BA17
237eoj_A_G23_G24NANNANT01.17BA10
247eoj_A_G24_G25NANNANT00.60AA01
257eoj_A_G25_C26NANNANT00.72AB02
267eoj_A_C26_G27AAAAA08700.26AA08
277eoj_A_G27_C28AAAAA00910.22AA00
287eoj_A_C28_C29OPNOP06260.67OP06
297eoj_A_C29_A30AAAAA00670.31AA00
307eoj_A_A30_A31AAAAA00620.35AA00
317eoj_A_A31_U32AAAAA00840.26AA00
327eoj_A_U32_C33NANNANT01.05IC07
337eoj_A_C33_G34AAAAA08320.57AA08
347eoj_A_G34_U35AAAAA00810.28AA00
357eoj_A_U35_A36OPNOP04910.17OP04
367eoj_A_A36_G37AAAAA00690.25AA00
377eoj_A_G37_C38AAAAA00900.12AA00
387eoj_A_C38_G39AAAAA00860.19AA00
397eoj_A_G39_U40AAAAA00840.24AA00
407eoj_A_U40_G41ICLIC04480.38IC04
417eoj_A_G41_U42NANNANT00.67OP22
427eoj_A_U42_C43NANNANT00.64OP26
437eoj_A_C43_G44AAwAA05590.33AA05
447eoj_A_G44_G45AAAAA00520.32AA00
457eoj_A_G45_C46AAAAA00910.14AA00
467eoj_A_C46_G47AAAAA00880.10AA00
477eoj_A_G47_C48AAAAA00920.13AA00
487eoj_A_C48_C49AAAAA00900.22AA00

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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