Resolution: 2.8→2.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.67 / % possible all: 99.7
-
Processing
Software
Name
Version
Classification
REFMAC
5.5.0109
refinement
HKL-3000
phasing
SHELXD
phasing
SHELXE
modelbuilding
MLPHARE
phasing
DM
modelbuilding
RESOLVE
modelbuilding
Coot
modelbuilding
ARP/wARP
modelbuilding
CNS
refinement
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
DM
phasing
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.78→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.939 / SU B: 33.164 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25743
900
5 %
RANDOM
Rwork
0.22547
-
-
-
obs
0.22724
16965
98.9 %
-
all
-
17864
-
-
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: 60.351 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.76 Å2
0 Å2
0.39 Å2
2-
-
3.03 Å2
0 Å2
3-
-
-
-5.65 Å2
Refinement step
Cycle: LAST / Resolution: 2.78→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3773
0
0
5
3778
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
3829
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.218
1.967
5181
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.464
5
474
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.249
24.94
166
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
18.968
15
659
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.739
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.081
0.2
620
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2803
X-RAY DIFFRACTION
r_gen_planes_other
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
2.25
1.5
2426
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
4.071
2
3890
X-RAY DIFFRACTION
r_scbond_it
2.116
3
1403
X-RAY DIFFRACTION
r_scangle_it
3.683
4.5
1291
X-RAY DIFFRACTION
r_rigid_bond_restr
1.542
3
3829
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.783→2.855 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.354
54
-
Rwork
0.275
1143
-
obs
-
-
98.2 %
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
1.9745
-0.6007
2.3988
3.9439
-6.9804
14.2722
0.0513
-0.2188
-0.0765
0.0423
-0.2878
-0.1852
-0.0254
0.274
0.2365
0.3834
-0.0391
0.0388
0.5242
-0.0183
0.4326
31.6475
59.2513
39.76
2
3.2378
0.0206
1.4727
2.1787
2.8789
4.5931
0.1333
-0.149
0.4145
-0.3107
-0.1748
-0.2405
-0.3957
-0.1169
0.0415
0.4277
-0.0407
0.0932
0.5203
0.0333
0.4382
30.078
82.5024
22.0009
3
7.9788
7.631
7.2787
7.3293
6.7573
8.8888
0.1875
-0.1575
0.4581
0.2408
-0.2255
0.4429
-0.0949
-0.3238
0.038
0.5219
0.0001
-0.0135
0.559
0.0171
0.5023
34.3939
81.0389
9.5271
4
5.5179
-1.0159
1.044
0.7823
-0.4334
1.8203
0.1222
-0.0627
0.0514
-0.1229
-0.0267
-0.124
0.0638
0.0192
-0.0956
0.4019
-0.0405
0.0695
0.506
0.0021
0.3933
32.7006
72.1235
14.7736
5
3.7788
-1.3844
9.2607
1.4021
-5.9018
29.793
-0.3014
-0.1778
0.1872
0.014
-0.0028
0.0067
-0.3741
-0.4108
0.3043
0.3336
-0.0236
0.0431
0.5545
0.0026
0.4405
21.3523
69.8014
23.5643
6
9.0799
-0.3793
5.1988
2.9503
-1.2629
4.5872
-0.3543
-0.1422
0.4744
-0.0676
-0.0349
-0.2227
-0.0767
0.1607
0.3892
0.4044
-0.018
0.0566
0.4931
0.0142
0.4007
41.2544
68.9909
44.1318
7
2.6743
6.6033
-1.1537
17.3851
-7.0104
18.1709
0.3639
-0.3491
-0.1357
1.172
-0.6161
-0.3696
-0.3744
0.0706
0.2523
0.3778
0.2431
0.0865
0.7873
-0.0243
0.2695
38.3442
71.5581
56.3479
8
0.3323
0.8789
-0.3333
3.523
0.0484
1.4105
-0.0109
-0.1005
0.0342
0.0074
0.0489
0.0608
0.0556
-0.0938
-0.038
0.3696
-0.0098
0.0525
0.6563
-0.0003
0.3676
32.5269
66.3662
51.0665
9
3.3887
-3.7826
-6.8774
6.8967
10.4409
22.715
-0.1162
0.0808
-0.0951
0.1627
-0.4085
0.4805
0.0602
-0.5156
0.5247
0.3681
-0.0446
0.0474
0.5182
0.0268
0.4412
13.3672
67.9476
36.0878
10
5.9031
-0.4238
-2.6955
4.3529
-0.1057
1.3022
-0.0726
-0.2046
-0.3293
-0.011
-0.0013
0.0978
0.1616
0.0382
0.0739
0.4655
-0.0391
-0.0081
0.5546
0.0233
0.393
20.6541
44.695
20.6938
11
7.8524
3.2819
-2.9089
2.5581
-1.6382
4.5003
-0.0316
0.5259
-0.1326
-0.0162
0.0831
-0.0041
0.147
-0.2034
-0.0516
0.4415
-0.0008
0.0441
0.4918
-0.0073
0.3971
20.7559
46.1766
7.2284
12
4.6057
-0.5844
0.8172
0.975
0.4745
0.5877
0.0447
-0.0757
0.1599
-0.0902
-0.0797
-0.0883
-0.032
0.1028
0.035
0.4345
-0.0592
0.0339
0.4987
0.0103
0.3407
21.3451
54.586
12.636
13
9.5143
-5.511
-12.5558
3.1949
7.2753
16.5742
-0.2458
-0.2481
-0.0831
0.1265
0.1498
0.0196
0.2852
0.328
0.096
0.3684
-0.037
0.0042
0.5504
0.0232
0.4049
28.7466
57.499
24.252
14
3.2139
-2.6248
0.746
2.6399
1.1318
6.3565
-0.002
-0.2942
-0.7907
0.0036
-0.0318
0.6773
0.1681
-0.9528
0.0337
0.4025
-0.0993
0.0676
0.6726
0.0213
0.5412
2.1855
58.5322
36.8044
15
3.6152
10.2567
5.9264
31.1579
15.4941
10.7464
-0.3144
0.1764
0.0589
-0.7295
0.5275
1.0187
-0.6937
0.5132
-0.2131
0.2819
0.0109
0.1234
0.786
0.1582
0.6664
0.8462
55.9176
49.5753
16
3.3428
-2.7027
-1.796
6.5209
0.8179
2.4696
-0.1422
-0.4288
-0.1699
0.0736
0.2374
0.1908
0.0222
0.1618
-0.0952
0.3687
-0.0297
0.0465
0.5844
0.0163
0.3518
8.6482
61.6486
46.3649
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-4 - 16
2
X-RAY DIFFRACTION
2
A
17 - 50
3
X-RAY DIFFRACTION
3
A
51 - 72
4
X-RAY DIFFRACTION
4
A
73 - 131
5
X-RAY DIFFRACTION
5
B
-4 - 16
6
X-RAY DIFFRACTION
6
B
17 - 50
7
X-RAY DIFFRACTION
7
B
51 - 72
8
X-RAY DIFFRACTION
8
B
73 - 131
9
X-RAY DIFFRACTION
9
C
-4 - 16
10
X-RAY DIFFRACTION
10
C
17 - 50
11
X-RAY DIFFRACTION
11
C
51 - 72
12
X-RAY DIFFRACTION
12
C
73 - 131
13
X-RAY DIFFRACTION
13
D
-4 - 16
14
X-RAY DIFFRACTION
14
D
17 - 50
15
X-RAY DIFFRACTION
15
D
51 - 72
16
X-RAY DIFFRACTION
16
D
73 - 131
+
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