Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Sequence details
RNA DERIVED FROM 252 NUCLEOTIDE TOXI NON-CODING RNA OF PECA1039 PLASMID. RNA BOUND CORRESPONDS TO ...RNA DERIVED FROM 252 NUCLEOTIDE TOXI NON-CODING RNA OF PECA1039 PLASMID. RNA BOUND CORRESPONDS TO NUCLEOTIDES 1775-1810 (WHICH IS 70-104 OF TOXI TRANSCRIPT) AND WHICH HAS UNDERGONE 3' HYDROLYSIS.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.7 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal grow
Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.6M NACL, 0.1M MES PH6.5, 20% W/V PEG 4000
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.873 Å / Relative weight: 1
Reflection
Resolution: 3→35 Å / Num. obs: 35628 / % possible obs: 89.7 % / Observed criterion σ(I): 3 / Redundancy: 6.2 % / Biso Wilson estimate: 50.38 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18
Reflection shell
Highest resolution: 3 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.4 / % possible all: 66.3
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE: 1.6_289)
refinement
DENZO
datareduction
SCALEPACK
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SEM MODEL OF TOXIN COMPLEX FROM SAME STUDY Resolution: 3→35 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 24.41 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.258
1734
4.9 %
Rwork
0.214
-
-
obs
0.216
35161
89.1 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.21 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Biso mean: 34.2 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.1438 Å2
-0 Å2
-0 Å2
2-
-
-12.8967 Å2
0 Å2
3-
-
-
-15.0855 Å2
Refinement step
Cycle: LAST / Resolution: 3→35 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7896
4584
0
171
12651
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
13194
X-RAY DIFFRACTION
f_angle_d
1.642
18846
X-RAY DIFFRACTION
f_dihedral_angle_d
20.321
5670
X-RAY DIFFRACTION
f_chiral_restr
0.082
2220
X-RAY DIFFRACTION
f_plane_restr
0.009
1608
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Number
Refine-ID
Type
Rms dev position (Å)
1
1
A
1307
X-RAY DIFFRACTION
POSITIONAL
1
2
B
1307
X-RAY DIFFRACTION
POSITIONAL
0.061
1
3
E
1307
X-RAY DIFFRACTION
POSITIONAL
0.066
1
4
X
1307
X-RAY DIFFRACTION
POSITIONAL
0.056
1
5
Y
1307
X-RAY DIFFRACTION
POSITIONAL
0.062
1
6
Z
1307
X-RAY DIFFRACTION
POSITIONAL
0.056
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.0002-3.0884
0.3519
93
0.3164
1921
X-RAY DIFFRACTION
63
3.0884-3.188
0.3562
95
0.3011
2099
X-RAY DIFFRACTION
68
3.188-3.3019
0.3246
121
0.2699
2247
X-RAY DIFFRACTION
73
3.3019-3.434
0.289
136
0.2475
2293
X-RAY DIFFRACTION
75
3.434-3.5901
0.2582
145
0.2409
2720
X-RAY DIFFRACTION
88
3.5901-3.7792
0.2568
148
0.2192
3075
X-RAY DIFFRACTION
99
3.7792-4.0157
0.2526
163
0.2002
3066
X-RAY DIFFRACTION
100
4.0157-4.3252
0.2366
166
0.1838
3125
X-RAY DIFFRACTION
100
4.3252-4.7595
0.2077
150
0.1709
3146
X-RAY DIFFRACTION
100
4.7595-5.446
0.2255
156
0.174
3168
X-RAY DIFFRACTION
100
5.446-6.8529
0.237
177
0.1935
3186
X-RAY DIFFRACTION
100
6.8529-35.0013
0.2278
184
0.1971
3381
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.893
0.6979
-0.2766
2.3555
-0.5531
1.1499
0.1476
0.2985
-0.0144
0.0089
-0.0061
0.2416
-0.0005
-0.1511
-0.0929
0.0048
0.064
0.0307
0.2008
0.0203
0.2223
-13.0107
-2.0302
111.7796
2
0.1704
-1.3298
-0.04
3.3035
0.0716
2.0203
-0.1173
-0.245
-0.1454
-0.0775
0.0414
-0.1283
-0.0389
-0.2112
0.0862
0.0444
-0.0039
0.0519
0.2329
0.0024
0.2694
-4.884
26.8585
66.3007
3
2.2148
0.47
1.2737
1.4068
-0.475
1.9006
-0.1264
-0.3035
0.2673
-0.4136
0.1115
-0.014
0.0819
-0.1131
0.0558
0.1372
0.0116
0.0381
0.0748
-0.0366
0.1469
-9.639
-26.9106
64.1372
4
-0.5591
0.4663
-0.9211
1.9824
3.4873
7.3997
-0.1855
0.0487
-0.1296
-0.0128
-0.1639
0.0546
-0.0506
-0.9814
0.386
0.225
0.2145
-0.0648
0.5106
-0.1285
0.3299
-5.4226
-20.3361
90.1717
5
-0.4528
0.6295
-0.68
2.6973
-2.865
5.1311
-0.154
0.1089
-0.0135
-0.0706
0.1967
-0.0194
-0.1857
-0.0782
-0.0224
0.2274
0.0233
0.001
0.5328
0.0921
0.2819
-3.3364
16.6447
93.834
6
-0.2919
0.6403
-0.7752
6.1598
1.0233
2.0902
-0.2801
0.0407
-0.2211
-0.2544
0.0596
-0.3118
0.6319
0.1194
0.2824
0.3615
-0.0842
0.1253
0.1905
-0.0324
0.6154
-0.9539
0.6019
60.7071
7
1.148
-0.3931
-0.3384
0.7682
0.6125
1.5835
0.5154
0.0537
-0.0383
-0.448
-0.0281
-0.0914
0.117
0.0154
-0.3679
1.3167
0.1716
-0.2659
0.6013
-0.1218
0.3642
5.6282
-0.6913
-16.5074
8
2.5588
0.8483
-0.4965
2.613
-0.8601
3.8797
0.0021
0.2441
0.0306
-0.2807
0.0201
0.0326
-0.9224
-0.1584
-0.0811
0.7556
-0.0371
0.1266
0.5061
-0.0801
0.336
-1.406
27.1334
29.2068
9
2.7518
1.106
0.4635
5.9433
-3.8247
6.9537
0.1815
-0.0414
0.3488
-1.2612
0.4854
0.8276
2.4645
0.6445
-0.45
1.0485
-0.1923
-0.3175
0.4878
0.0989
0.3613
6.7897
-26.488
31.3791
10
-0.6176
-0.0147
-0.0779
3.0265
-0.7622
1.502
0.5107
-0.2582
0.2261
-1.8123
-0.134
-0.3051
-0.5929
1.11
0.4459
1.4607
-0.6252
-0.8699
1.1594
0.4559
0.2779
-0.8549
-20.3693
6.0559
11
0.3772
-0.4409
-0.4315
1.6684
1.4111
1.9849
0.3941
-0.3457
0.0803
-0.5932
-0.1722
-0.051
-1.0752
-0.6181
-0.1668
1.3344
0.0428
-0.0755
0.9012
-0.1339
0.4566
-3.786
17.5672
1.7458
12
2.6945
-1.5111
-0.1738
2.0113
-2.1455
3.6178
-0.4073
-0.045
-0.5056
-0.4429
0.0669
-0.1322
0.4804
-0.2745
0.2253
0.6293
-0.1075
0.1605
0.3871
-0.1435
0.5008
-3.646
0.7908
34.7538
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINA
2
X-RAY DIFFRACTION
2
CHAINB
3
X-RAY DIFFRACTION
3
CHAINE
4
X-RAY DIFFRACTION
4
CHAING
5
X-RAY DIFFRACTION
5
CHAINH
6
X-RAY DIFFRACTION
6
CHAINI
7
X-RAY DIFFRACTION
7
CHAINX
8
X-RAY DIFFRACTION
8
CHAINY
9
X-RAY DIFFRACTION
9
CHAINZ
10
X-RAY DIFFRACTION
10
CHAINU
11
X-RAY DIFFRACTION
11
CHAINV
12
X-RAY DIFFRACTION
12
CHAINW
+
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