Method to determine structure: MOLECULAR REPLACEMENT Starting model: in-house model Resolution: 2.54→87.7 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / SU B: 17.771 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 1.341 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26859
2372
5.2 %
RANDOM
Rwork
0.20474
-
-
-
obs
0.20813
43188
86.11 %
-
all
-
53194
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 43.273 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.72 Å2
0 Å2
0 Å2
2-
-
-1.13 Å2
0 Å2
3-
-
-
0.41 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.3338 Å
0.3338 Å
Luzzati d res low
-
0.3338 Å
Luzzati sigma a
0.3338 Å
0.3338 Å
Refinement step
Cycle: LAST / Resolution: 2.54→87.7 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9987
0
217
142
10346
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
10332
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
6704
X-RAY DIFFRACTION
r_angle_refined_deg
1.402
2
14020
X-RAY DIFFRACTION
r_angle_other_deg
0.915
3
16346
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.148
5
1350
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.63
23.575
400
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.686
15
1671
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
23.843
15
85
X-RAY DIFFRACTION
r_chiral_restr
0.076
0.2
1663
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
11528
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
2030
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.506
1.5
6667
X-RAY DIFFRACTION
r_mcbond_other
0.065
1.5
2858
X-RAY DIFFRACTION
r_mcangle_it
0.932
2
10584
X-RAY DIFFRACTION
r_scbond_it
1.136
3
3665
X-RAY DIFFRACTION
r_scangle_it
1.916
4.5
3436
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.54→2.604 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.301
14
-
Rwork
0.338
311
-
obs
-
-
8.37 %
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
0.7975
0.0553
0.4093
0.8961
-0.6018
0.8559
-0.0316
0.0357
0.0101
0.0446
-0.0054
-0.0368
-0.011
-0.0183
0.037
0.0739
-0.0352
-0.0002
0.1253
0.0117
0.0741
69.6831
17.9805
24.3794
2
0.3466
0.1082
0.1173
1.0231
-0.2818
1.7654
0.0033
-0.0725
0.0093
0.0071
-0.0587
0.0411
-0.0963
-0.0517
0.0553
0.0712
-0.0186
0.0276
0.146
-0.0107
0.0693
63.8708
32.7655
50.4923
3
0.4815
-0.1957
0.4671
1.0134
-0.1859
1.7534
0.0366
-0.003
0.0215
-0.0535
0.0016
-0.0083
-0.0349
0.1775
-0.0382
0.071
-0.0742
0.0208
0.1662
-0.0243
0.0499
96.3682
45.7348
46.4041
4
1.1874
0.3962
0.6696
0.5874
-0.2776
1.9237
0.0336
0.0122
-0.085
-0.018
0.0045
-0.0406
-0.2084
0.0451
-0.0381
0.1028
-0.0586
0.0259
0.1472
-0.0308
0.0403
97.6781
37.5703
22.5679
5
1.0824
0.4102
0.8717
0.8566
0.2408
1.8129
0.0784
-0.0744
-0.1036
0.0248
0.0654
-0.1534
0.091
-0.0239
-0.1438
0.05
-0.0089
-0.0335
0.0963
0.029
0.126
89.1056
12.4204
38.612
6
1.275
0.0736
0.0381
0.8526
-0.1137
1.5309
-0.0042
0.0036
0.1446
-0.1368
0.003
0.0849
-0.0692
-0.0566
0.0012
0.1478
0.0003
-0.0292
0.0835
0.0159
0.0943
68.0522
51.1308
34.4693
7
1.9075
0.0101
0.775
1.2321
0.8843
2.9105
0.0757
-0.0338
-0.0271
0.0304
-0.0042
0.2227
0.2918
-0.3977
-0.0715
0.0519
-0.0958
-0.0078
0.179
0.0107
0.0928
50.4143
13.176
22.4329
8
2.9478
0.7358
-0.1202
1.3415
1.464
1.9741
0.0187
-0.1437
-0.1868
-0.0092
-0.1371
0.1699
0.017
-0.2678
0.1185
0.0799
-0.0346
0.026
0.1603
0.0896
0.1624
49.2484
20.4828
54.3779
9
2.5541
0.0303
0.3166
2.1575
-0.2586
1.9594
0.3236
-0.2253
0.3464
-0.0428
-0.1009
0.0299
-0.4205
0.2989
-0.2227
0.1633
-0.0987
0.0947
0.1351
-0.1249
0.114
95.7471
63.1836
56.1222
10
2.6221
-0.7599
-0.1722
1.3395
-0.1829
1.3298
-0.0235
0.2398
-0.2412
0.0024
0.0513
-0.0915
-0.0618
0.0905
-0.0278
0.0245
-0.0524
0.0448
0.2085
-0.1035
0.0962
111.8542
26.3921
12.7129
11
1.4077
-1.9259
0.3866
2.8645
0.5971
3.6212
0.5041
0.0598
-0.2078
0.0362
0.2096
-0.318
0.6904
0.8558
-0.7137
0.2192
0.1806
-0.3481
0.1944
-0.1845
0.4553
106.3195
5.5728
37.9342
12
1.6971
1.0424
-0.0746
4.1102
0.1219
0.6111
-0.0119
-0.0624
0.4935
-0.1302
-0.0186
0.0307
-0.2092
-0.0226
0.0306
0.1995
0.013
-0.0153
0.0088
-0.005
0.1713
71.4323
69.9231
35.6224
13
0.2119
0.1469
-0.1018
0.0959
-0.0159
0.2384
0.0095
0.0244
-0.0139
0.0171
-0.0387
-0.0128
-0.045
-0.0306
0.0292
0.0522
-0.0042
0.0077
0.2144
0.0398
0.0759
75.5614
32.4455
38.9326
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
29 - 176
2
X-RAY DIFFRACTION
1
A
262
3
X-RAY DIFFRACTION
2
B
29 - 176
4
X-RAY DIFFRACTION
2
B
262 - 263
5
X-RAY DIFFRACTION
3
C
29 - 176
6
X-RAY DIFFRACTION
3
C
262
7
X-RAY DIFFRACTION
4
D
29 - 176
8
X-RAY DIFFRACTION
4
D
262
9
X-RAY DIFFRACTION
5
E
29 - 176
10
X-RAY DIFFRACTION
5
E
262
11
X-RAY DIFFRACTION
6
F
29 - 176
12
X-RAY DIFFRACTION
6
F
262
13
X-RAY DIFFRACTION
7
A
177 - 261
14
X-RAY DIFFRACTION
8
B
177 - 261
15
X-RAY DIFFRACTION
9
C
177 - 261
16
X-RAY DIFFRACTION
10
D
177 - 261
17
X-RAY DIFFRACTION
11
E
177 - 261
18
X-RAY DIFFRACTION
12
F
177 - 261
19
X-RAY DIFFRACTION
13
W
9 - 516
+
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