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

©Jiří Černý & Bohdan Schneider

Crystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA

Results of the assignment of 56 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
014rd5_C_DC2_DC3NANNANT00.55AA10
024rd5_C_DC3_DT4NANNANT00.53AA08
034rd5_C_DT4_DA5BBwBB16350.56BB16
044rd5_C_DA5_DA6BBBBB00310.41BB00
054rd5_C_DA6_DG7BB2BB07440.25BB07
064rd5_C_DG7_DC8BBBBB00740.31BB00
074rd5_C_DC8_DG9BB2BB07690.21BB07
084rd5_C_DG9_DG10BBBBB00820.20BB00
094rd5_C_DG10_DC11BB2BB07760.23BB07
104rd5_C_DC11_DA12BBBBB00690.37BB00
114rd5_C_DA12_DA13BB2BB07860.12BB07
124rd5_C_DA13_DT14B-ABA05720.14BA05
134rd5_C_DT14_DC15A-BAB03730.20AB03
144rd5_C_DC15_DC16NANNANT00.50BA09
154rd5_D_DG17_DG18AAAAA00620.28AA00
164rd5_D_DG18_DG19A-BAB05450.22AB05
174rd5_D_DG19_DA20NANNANT00.33BB10
184rd5_D_DA20_DT21BBBBB01480.20BB01
194rd5_D_DT21_DT22BBBBB00500.22BB00
204rd5_D_DT22_DG23NANNANT00.43BB08
214rd5_D_DG23_DC24B-ABA05510.37BA05
224rd5_D_DC24_DC25BBBBB01310.34BB01
234rd5_D_DC25_DG26BBBBB00700.25BB00
244rd5_D_DG26_DC27BB2BB07690.29BB07
254rd5_D_DC27_DT28BBBBB00490.30BB00
264rd5_D_DT28_DT29BB2BB07310.35BB07
274rd5_D_DT29_DA30BB2BB07770.18BB07
284rd5_D_DA30_DG31miBBB10430.26BB10
294rd5_E_DC2_DC3BBwBB17290.34BB17
304rd5_E_DC3_DT4BBBBB00750.26BB00
314rd5_E_DT4_DA5miBBB10330.29BB10
324rd5_E_DA5_DA6BBBBB00670.30BB00
334rd5_E_DA6_DG7BB2BB07530.23BB07
344rd5_E_DG7_DC8BBBBB00400.33BB00
354rd5_E_DC8_DG9BB2BB07700.26BB07
364rd5_E_DG9_DG10BBBBB00830.21BB00
374rd5_E_DG10_DC11BB2BB07620.34BB07
384rd5_E_DC11_DA12BBBBB00640.43BB00
394rd5_E_DA12_DA13BB2BB07230.24BB07
404rd5_E_DA13_DT14B-ABA10700.31BA10
414rd5_E_DT14_DC15NANNANT00.72AA10
424rd5_E_DC15_DC16BBwBB16590.32BB16
434rd5_F_DG17_DG18NANNANT00.41BB13
444rd5_F_DG18_DG19NANNANT00.44BB10
454rd5_F_DG19_DA20miBBB14250.30BB14
464rd5_F_DA20_DT21BBBBB00370.36BB00
474rd5_F_DT21_DT22NANNANT00.46BB05
484rd5_F_DT22_DG23NANNANT00.38BB08
494rd5_F_DG23_DC24B-ABA05290.38BA05
504rd5_F_DC24_DC25A-BAB03660.35AB03
514rd5_F_DC25_DG26BBBBB00850.20BB00
524rd5_F_DG26_DC27BB2BB07800.30BB07
534rd5_F_DC27_DT28BBwBB02130.38BB02
544rd5_F_DT28_DT29BBBBB00100.41BB00
554rd5_F_DT29_DA30B12BB04460.33BB04
564rd5_F_DA30_DG31BBwBB02540.43BB02

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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