Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
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Details
Compound details
ENGINEERED RESIDUE IN CHAIN X, A 2542 TO U ENGINEERED RESIDUE IN CHAIN X, G 2543 TO C ENGINEERED ...ENGINEERED RESIDUE IN CHAIN X, A 2542 TO U ENGINEERED RESIDUE IN CHAIN X, G 2543 TO C ENGINEERED RESIDUE IN CHAIN X, U 2544 TO C ENGINEERED RESIDUE IN CHAIN Z, C 2550 TO G ENGINEERED RESIDUE IN CHAIN Z, U 2551 TO A
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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: 1.5 Å3/Da / Density % sol: 64 % Description: DATA WAS COLLECTED BY ANNIE HEROUX AS PART OF THE MACROMOLECULAR CRYSTALLOGRAPHY RESEARCH RESOURCE AT BROOKHAVEN NSLS
Crystal grow
Details: RNA WAS CRYSTALLIZED FROM 15% PEG-MONOMETHYL 550 ETHER, 0.1 M MGCL2, 0.05 M NA-HEPES PH 7.0, 1 MM FMN
Resolution: 2.941→26.292 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 24.5 / Stereochemistry target values: ML Details: THE GAMMA PHOSPHATE OF GTP IS DISORDERED ON CHAINS X AND Z
Rfactor
Num. reflection
% reflection
Rfree
0.2314
507
5.3 %
Rwork
0.2041
-
-
obs
0.2056
9559
98.03 %
Solvent computation
Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.744 Å2 / ksol: 0.247 e/Å3
Displacement parameters
Biso mean: 96.2 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-6.6226 Å2
0 Å2
0 Å2
2-
-
-6.6226 Å2
0 Å2
3-
-
-
13.2451 Å2
Refinement step
Cycle: LAST / Resolution: 2.941→26.292 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
0
2394
47
29
2470
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
2730
X-RAY DIFFRACTION
f_angle_d
0.612
4261
X-RAY DIFFRACTION
f_dihedral_angle_d
24.223
1379
X-RAY DIFFRACTION
f_chiral_restr
0.056
556
X-RAY DIFFRACTION
f_plane_restr
0.005
112
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.9415-3.3664
0.3216
165
0.2639
2919
X-RAY DIFFRACTION
97
3.3664-4.2384
0.2204
163
0.2005
3006
X-RAY DIFFRACTION
99
4.2384-26.2933
0.2162
179
0.1911
3127
X-RAY DIFFRACTION
98
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
1.2494
1.1174
-0.0151
8.319
-1.4755
0.2562
0.1555
1.9402
0.7914
-0.44
0.3006
1.9285
0.289
2.2825
-0.317
0.7305
-0.1247
0.2952
2.3537
-0.3735
1.5153
6.8853
-62.881
-58.7253
2
0.954
0.2247
0.0632
0.8402
0.247
0.8198
-0.1855
0.2348
-0.2243
-0.0193
0.2102
0.0048
0.7215
-0.3192
-0.066
0.7719
-0.0698
-0.0554
0.7859
-0.0158
0.5534
27.305
-58.91
-71.5769
3
3.799
0.5282
-0.5077
1.213
1.0356
2.5729
0.065
-0.7587
1.4197
-0.0356
-0.1216
0.495
-0.4135
0.2492
0.0035
0.3626
-0.0585
0.0799
0.3714
-0.1083
0.4612
28.935
-44.7541
-80.8539
4
1.8644
-1.0002
-0.0341
1.2484
-1.2305
0.9681
0.0874
-0.0709
0.1701
-0.2482
0.0379
0.0502
0.4192
0.1422
-0.015
0.7615
-0.0036
0.0274
0.6762
0.0137
0.6258
18.5514
-76.1059
-75.6039
5
0.2093
0.1547
0.5002
1.8212
0.487
0.7906
0.1665
-0.2261
-0.7776
-0.07
-0.3998
1.2533
0.225
-0.9875
0.0273
0.6922
0.1598
-0.0214
1.0212
0.0779
1.3457
-0.6527
-65.4455
-77.1439
6
6.0776
5.3235
0.1629
5.3655
1.3098
2.1374
0.4044
0.0691
0.9332
1.5368
-1.1105
1.8959
0.2776
0.7149
-0.0845
1.077
0.3964
-0.1189
0.686
0.0082
1.3655
-13.1103
-46.4331
-81.9627
7
1.9703
-2.876
-1.3283
5.1377
3.2657
2.5708
-1.1927
0.4362
-0.1583
1.297
-0.191
1.3605
-0.1984
0.0959
0.6283
2.44
0.2883
-0.1985
0.9625
0.1294
1.4851
-11.8801
-48.8534
-75.1036
8
2.1932
2.128
0.1882
2.2652
0.0176
0.1501
1.0522
-0.6011
-0.4799
0.3017
-0.6791
-0.4102
0.0693
-0.197
-0.0614
0.6266
0.1358
-0.2954
1.2454
0.1638
1.2216
-5.4727
-61.0906
-84.3032
9
0.5725
-0.2901
-0.2845
0.9294
0.7536
0.7896
-0.1864
-0.03
-0.0653
0.3239
0.0377
0.0225
0.5285
0.2747
0.0916
0.7529
0.1533
-0.0559
0.6518
-0.0081
0.616
22.8874
-80.1053
-86.2377
10
1.0551
-0.9415
0.1443
0.3412
-0.0366
0.4629
-0.0313
0.3074
0.0762
0.2494
0.23
0.0142
-0.0162
0.0313
-0.0542
0.5135
0.0952
-0.0819
0.4858
-0.0717
0.4845
24.9118
-80.7683
-82.2455
11
1.8636
0.433
-1.4078
0.4078
0.1618
1.8002
0.0629
-0.2022
0.0868
-0.0423
0.1609
-0.092
-0.4923
0.0467
-0.1412
0.671
0.0525
0.0306
0.6637
0.0037
0.7
13.7694
-54.3297
-74.3904
12
3.1116
0.6692
-2.2274
0.6152
-0.3502
1.6284
0.639
-1.4264
-0.6753
0.1715
0.4721
0.4956
-0.2259
-0.9746
0.44
0.5309
-0.075
0.322
1.3553
0.2745
0.686
2.0883
-70.7748
-57.4857
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINZANDRESID57:61)
2
X-RAY DIFFRACTION
2
(CHAINZANDRESID62:66)
3
X-RAY DIFFRACTION
3
(CHAINZANDRESID67:78)
4
X-RAY DIFFRACTION
4
(CHAINZANDRESID79:98)
5
X-RAY DIFFRACTION
5
(CHAINZANDRESID99:106)
6
X-RAY DIFFRACTION
6
(CHAINZANDRESID107:113)
7
X-RAY DIFFRACTION
7
(CHAINXANDRESID1:5)
8
X-RAY DIFFRACTION
8
(CHAINXANDRESID6:9)
9
X-RAY DIFFRACTION
9
(CHAINXANDRESID10:19)
10
X-RAY DIFFRACTION
10
(CHAINXANDRESID20:32)
11
X-RAY DIFFRACTION
11
(CHAINXANDRESID33:48)
12
X-RAY DIFFRACTION
12
(CHAINXANDRESID49:54)
+
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