Resolution: 2.45→2.54 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 2 / Num. unique all: 6192 / Rsym value: 0.942 / % possible all: 99.4
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
PHENIX
modelbuilding
REFMAC
5.5.0109
refinement
DENZO
datareduction
SCALEPACK
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.45→40 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 15.503 / SU ML: 0.162 Isotropic thermal model: isotropic atomic model plus TLS anisotropic model for domains Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.231 / Stereochemistry target values: Engh & Huber Details: TLSANL was used to determine the TLS-anisotropic components of temperature factors for all atoms as obtained by refining TLS parameters for individual domains
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22228
3195
5.1 %
RANDOM
Rwork
0.18463
-
-
-
all
0.18657
59863
-
-
obs
0.18657
59863
99.92 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 56.18 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.45 Å2
0 Å2
0 Å2
2-
-
-1.45 Å2
0 Å2
3-
-
-
2.91 Å2
Refinement step
Cycle: LAST / Resolution: 2.45→40 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
9966
0
30
412
10408
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
10259
X-RAY DIFFRACTION
r_angle_refined_deg
1.054
1.947
13974
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.52
5
1256
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.229
22.75
480
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.935
15
1630
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.474
15
96
X-RAY DIFFRACTION
r_chiral_restr
0.073
0.2
1526
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.021
7930
X-RAY DIFFRACTION
r_mcbond_it
1.289
2
6300
X-RAY DIFFRACTION
r_mcangle_it
2.231
2.5
10176
X-RAY DIFFRACTION
r_scbond_it
3.245
3.5
3959
X-RAY DIFFRACTION
r_scangle_it
4.936
4.5
3798
LS refinement shell
Resolution: 2.451→2.514 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.296
229
-
Rwork
0.243
4345
-
obs
-
4345
99.22 %
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
0.7443
0.0373
0.4361
0.8711
0.3697
1.0093
-0.0306
-0.1162
-0.0417
0.0473
0.0535
0.1172
0.0302
-0.1265
-0.0229
0.0475
-0.0189
-0.0001
0.0683
0.0346
0.0525
129.06
62.994
64.733
2
1.4639
-0.2494
0.2017
1.412
0.2737
0.9548
0.0773
-0.083
-0.4598
0.0004
0.0538
0.1262
0.1888
0.0018
-0.1312
0.0762
-0.0268
-0.0649
0.0238
0.0374
0.1853
132.637
40.267
53.361
3
5.3312
-0.1934
-1.7911
0.3315
0.0181
2.2163
0.2358
0.6595
-0.6651
-0.2604
-0.2015
0.273
0.2806
-0.0397
-0.0343
0.3442
0.1365
-0.2402
0.2259
-0.2533
0.3521
140.265
30.83
31.001
4
3.0095
0.0292
1.0825
1.6432
1.8196
3.4481
0.2017
0.5417
0.0349
-0.3912
-0.1096
0.0726
-0.2826
0.1464
-0.0922
0.1683
0.1001
-0.0331
0.178
-0.0605
0.0778
164.139
43.341
29.273
5
0.7125
0.318
-0.2072
0.7567
-0.4865
1.1419
-0.0407
-0.0542
0.0089
0.0136
-0.0295
-0.0305
-0.0431
0.1717
0.0702
0.0453
-0.0175
0.0089
0.0751
0.0102
0.0372
96.351
13.369
46.687
6
1.1295
0.1413
-0.111
1.3083
-0.2711
1.3887
-0.0121
0.0635
0.2067
-0.0318
0.0131
0.0489
-0.3247
0.0343
-0.0011
0.1515
-0.0459
-0.0184
0.041
0.0404
0.0689
91.907
36.065
35.44
7
4.8448
0.4392
1.1652
0.7142
-0.5798
2.5484
-0.1152
0.7586
0.3382
-0.2016
0.0276
-0.0395
-0.3175
-0.0527
0.0876
0.424
-0.0267
-0.0239
0.2838
0.1805
0.1629
83.86
45.2
13.047
8
3.9559
1.3164
-0.4031
2.7852
-0.5525
4.0617
-0.2145
0.995
-0.1437
-0.3818
0.2867
0.1438
0.1356
-0.0979
-0.0722
0.2899
0.0145
-0.0762
0.3931
0.0087
0.068
60.603
31.461
11.205
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 157
2
X-RAY DIFFRACTION
2
A
158 - 405
3
X-RAY DIFFRACTION
3
A
406 - 492
4
X-RAY DIFFRACTION
3
A
580 - 629
5
X-RAY DIFFRACTION
4
A
493 - 579
6
X-RAY DIFFRACTION
5
B
1 - 157
7
X-RAY DIFFRACTION
6
B
158 - 405
8
X-RAY DIFFRACTION
7
B
406 - 492
9
X-RAY DIFFRACTION
7
B
580 - 629
10
X-RAY DIFFRACTION
8
B
493 - 579
+
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