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Conformers: ABBIImiBZICOPNSYNN
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SAM-II riboswitch bound to S-adenosylmethionine

Results of the assignment of 153 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 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 numberStep nameCANANtCconfalrmsd
0012qwy_A_G1_C2AAAAA08160.41 AA08
0022qwy_A_C2_G3AAAAA00680.15 AA00
0032qwy_A_G3_C4AAAAA03780.28 AA03
0042qwy_A_C4_G5AAwAA06670.28 AA06
0052qwy_A_G5_G6AAAAA00420.29 AA00
0062qwy_A_G6_C7AAAAA00690.19 AA00
0072qwy_A_C7_G8ICLIC01540.24 IC01
0082qwy_A_G8_A9B-ABA13600.32 BA13
0092qwy_A_A9_U10AAAAA00210.24 AA00
0102qwy_A_U10_U11AAAAA00720.30 AA00
0112qwy_A_U11_U12AAAAA00810.28 AA00
0122qwy_A_U12_A13NANNANT00.47 IC01
0132qwy_A_A13_A14NANNANT01.82 OP06
0142qwy_A_A14_C15NANNANT01.16 OP29
0152qwy_A_C15_C16AAAAA00750.22 AA00
0162qwy_A_C16_G17AAAAA08390.45 AA08
0172qwy_A_G17_U18AAuAA07480.51 AA07
0182qwy_A_U18_A19AAAAA04500.52 AA04
0192qwy_A_A19_U20AAAAA00190.45 AA00
0202qwy_A_U20_U21AAAAA00780.12 AA00
0212qwy_A_U21_G22NANNANT00.67 AA12
0222qwy_A_G22_C23AAAAA08740.24 AA08
0232qwy_A_C23_A24AAAAA00450.32 AA00
0242qwy_A_A24_G25AAAAA04830.25 AA04
0252qwy_A_G25_U26AAAAA08910.22 AA08
0262qwy_A_U26_C27AAAAA00670.21 AA00
0272qwy_A_C27_G28NANNANT00.47 AA08
0282qwy_A_G28_C29AAAAA08840.13 AA08
0292qwy_A_C29_G30NANNANT00.59 AB03
0302qwy_A_G30_U31NANNANT01.18 OP21
0312qwy_A_U31_G32NANNANT01.46 OP19
0322qwy_A_G32_A33NANNANT01.01 ZZ02
0332qwy_A_A33_U34NANNANT00.70 OP14
0342qwy_A_U34_A35NANNANT01.69 OP01
0352qwy_A_A35_A36AAAAA04310.44 AA04
0362qwy_A_A36_A37AAAAA00610.22 AA00
0372qwy_A_A37_U38AAwAA01740.25 AA01
0382qwy_A_U38_G39AAAAA00110.60 AA00
0392qwy_A_G39_U40NANNANT01.89 IC04
0402qwy_A_U40_A41NANNANT01.09 BA16
0412qwy_A_A41_G42AAwAA05500.23 AA05
0422qwy_A_G42_C43AAAAA00380.32 AA00
0432qwy_A_C43_U44AAAAA00660.15 AA00
0442qwy_A_U44_A45AAwAA10480.31 AA10
0452qwy_A_A45_A46AAAAA00660.19 AA00
0462qwy_A_A46_A47AAAAA08140.57 AA08
0472qwy_A_A47_A48OPNOP07610.29 OP07
0482qwy_A_A48_A49AAAAA00490.40 AA00
0492qwy_A_A49_G50AAAAA08400.50 AA08
0502qwy_A_G50_G51AAAAA00590.23 AA00
0512qwy_A_G51_A52NANNANT00.53 IC03
0522qwy_B_G1_C2AAAAA00430.28 AA00
0532qwy_B_C2_G3AAAAA00660.15 AA00
0542qwy_B_G3_C4AAAAA00720.16 AA00
0552qwy_B_C4_G5AAAAA08380.41 AA08
0562qwy_B_G5_G6AAAAA00280.33 AA00
0572qwy_B_G6_C7AAAAA00580.20 AA00
0582qwy_B_C7_G8NANNANT00.47 AA12
0592qwy_B_G8_A9AAwAA01330.48 AA01
0602qwy_B_A9_U10AAAAA00820.24 AA00
0612qwy_B_U10_U11AAAAA00800.31 AA00
0622qwy_B_U11_U12AAAAA00820.28 AA00
0632qwy_B_U12_A13NANNANT00.45 IC01
0642qwy_B_A13_A14NANNANT01.67 OP06
0652qwy_B_A14_C15NANNANT01.16 OP30
0662qwy_B_C15_C16AAAAA08280.35 AA08
0672qwy_B_C16_G17A-BAB05530.56 AB05
0682qwy_B_G17_U18NANNANT00.55 OP26
0692qwy_B_U18_A19AAAAA03870.18 AA03
0702qwy_B_A19_U20AAAAA00410.36 AA00
0712qwy_B_U20_U21AAAAA00150.30 AA00
0722qwy_B_U21_G22NANNANT00.78 AA12
0732qwy_B_G22_C23AAAAA00730.23 AA00
0742qwy_B_C23_A24AAwAA05340.50 AA05
0752qwy_B_A24_G25AAAAA08730.31 AA08
0762qwy_B_G25_U26AAAAA00700.28 AA00
0772qwy_B_U26_C27AAAAA00420.20 AA00
0782qwy_B_C27_G28NANNANT00.51 AA08
0792qwy_B_G28_C29AAAAA08780.19 AA08
0802qwy_B_C29_G30A-BAB05860.30 AB05
0812qwy_B_G30_U31NANNANT00.92 OP21
0822qwy_B_U31_G32NANNANT01.27 OP19
0832qwy_B_G32_A33NANNANT01.06 ZZ02
0842qwy_B_A33_U34NANNANT00.75 OP14
0852qwy_B_U34_A35NANNANT01.91 OP16
0862qwy_B_A35_A36AAAAA08760.30 AA08
0872qwy_B_A36_A37AAAAA00670.29 AA00
0882qwy_B_A37_U38AAAAA04720.30 AA04
0892qwy_B_U38_G39NANNANT00.53 AB05
0902qwy_B_G39_U40NANNANT01.26 OP22
0912qwy_B_U40_A41NANNANT01.08 OP27
0922qwy_B_A41_G42NANNANT01.04 AA11
0932qwy_B_G42_C43AAAAA0080.45 AA00
0942qwy_B_C43_U44AAAAA00740.15 AA00
0952qwy_B_U44_A45AAwAA01610.44 AA01
0962qwy_B_A45_A46AAAAA00180.32 AA00
0972qwy_B_A46_A47AAAAA00500.45 AA00
0982qwy_B_A47_A48OPNOP08570.21 OP08
0992qwy_B_A48_A49NANNANT00.76 AA08
1002qwy_B_A49_G50AAwAA01540.37 AA01
1012qwy_B_G50_G51AAAAA08640.29 AA08
1022qwy_B_G51_A52NANNANT00.44 IC02
1032qwy_C_G1_C2AAAAA00360.30 AA00
1042qwy_C_C2_G3AAAAA00720.15 AA00
1052qwy_C_G3_C4AAAAA00910.17 AA00
1062qwy_C_C4_G5NANNANT00.60 AA10
1072qwy_C_G5_G6AAAAA08100.39 AA08
1082qwy_C_G6_C7AAAAA08800.21 AA08
1092qwy_C_C7_G8NANNANT00.53 AA12
1102qwy_C_G8_A9AAwAA01330.48 AA01
1112qwy_C_A9_U10AAAAA00670.27 AA00
1122qwy_C_U10_U11AAAAA04810.36 AA04
1132qwy_C_U11_U12AAAAA08780.20 AA08
1142qwy_C_U12_A13NANNANT00.35 IC03
1152qwy_C_A13_A14NANNANT01.54 OP06
1162qwy_C_A14_C15NANNANT00.96 OP30
1172qwy_C_C15_C16AAAAA00640.27 AA00
1182qwy_C_C16_G17AAAAA08220.52 AA08
1192qwy_C_G17_U18AAuAA12710.41 AA12
1202qwy_C_U18_A19AAAAA00660.17 AA00
1212qwy_C_A19_U20AAAAA08620.39 AA08
1222qwy_C_U20_U21AAAAA03850.20 AA03
1232qwy_C_U21_G22NANNANT00.63 AA12
1242qwy_C_G22_C23AAAAA00490.25 AA00
1252qwy_C_C23_A24NANNANT00.47 AA06
1262qwy_C_A24_G25AAAAA08830.24 AA08
1272qwy_C_G25_U26AAAAA08420.23 AA08
1282qwy_C_U26_C27AAAAA04820.18 AA04
1292qwy_C_C27_G28NANNANT00.55 AA08
1302qwy_C_G28_C29AAAAA08680.24 AA08
1312qwy_C_C29_G30NANNANT00.38 AB04
1322qwy_C_G30_U31NANNANT01.90 OP13
1332qwy_C_U31_G32NANNANT01.45 OP19
1342qwy_C_G32_A33NANNANT01.14 ZZ02
1352qwy_C_A33_U34NANNANT00.70 OP14
1362qwy_C_U34_A35NANNANT01.72 OP16
1372qwy_C_A35_A36AAAAA08580.32 AA08
1382qwy_C_A36_A37AAAAA00480.25 AA00
1392qwy_C_A37_U38AAwAA01240.47 AA01
1402qwy_C_U38_G39AAAAA08140.76 AA08
1412qwy_C_G39_U40NANNANT01.11 OP02
1422qwy_C_U40_A41NANNANT01.22 AA11
1432qwy_C_A41_G42AAAAA0860.71 AA08
1442qwy_C_G42_C43AAAAA03700.35 AA03
1452qwy_C_C43_U44AAAAA00870.17 AA00
1462qwy_C_U44_A45AAwAA01710.38 AA01
1472qwy_C_A45_A46AAAAA00630.25 AA00
1482qwy_C_A46_A47AAAAA08740.42 AA08
1492qwy_C_A47_A48OPNOP08710.21 OP08
1502qwy_C_A48_A49NANNANT00.76 AA08
1512qwy_C_A49_G50AAAAA00140.50 AA00
1522qwy_C_G50_G51AAAAA00240.29 AA00
1532qwy_C_G51_A52ICLIC01680.22 IC01

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.
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).

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