Resolution: 1.5→20 Å / Num. obs: 115663 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.51 % / Biso Wilson estimate: 20.28 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.79
Reflection shell
Resolution: 1.5→1.6 Å / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
SHELX
phasing
REFMAC
refinement
PDB_EXTRACT
3.004
dataextraction
ProDC
datacollection
SHELXD
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.5→19.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.756 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20117
2983
5.1 %
RANDOM
Rwork
0.17648
-
-
-
obs
0.17774
59035
99.5 %
-
all
-
59035
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 15.948 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
-0.01 Å2
2-
-
-0.01 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.5→19.96 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3261
0
77
225
3563
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
3556
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.605
2.004
4851
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.567
5
452
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.093
23.797
158
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.269
15
599
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.614
15
30
X-RAY DIFFRACTION
r_chiral_restr
0.104
0.2
532
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
2748
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.244
0.2
1678
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.309
0.2
2475
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.142
0.2
248
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.884
0.2
4
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.209
0.2
138
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.175
0.2
18
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
0.94
1.5
2185
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.639
2
3536
X-RAY DIFFRACTION
r_scbond_it
2.691
3
1414
X-RAY DIFFRACTION
r_scangle_it
4.217
4.5
1315
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.5→1.539 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.275
190
-
Rwork
0.204
4048
-
obs
-
-
98.38 %
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
0.5902
0.0869
0.2428
1.2777
0.3158
1.0556
-0.0323
0.0834
-0.0193
-0.0362
0.0567
-0.0948
0.0302
0.1194
-0.0244
-0.0466
0.0072
0.0279
0.027
0.0108
-0.0017
4.696
11.836
17.966
2
0.3449
-0.2638
-0.4792
0.4689
1.3792
4.5043
0.1566
0.0043
0.0358
0.0134
0.1352
-0.165
0.0288
0.2851
-0.2918
0.0101
0.042
0.0236
0.0267
-0.0364
0.0287
4.491
-0.067
10.289
3
0.374
-0.2
-0.2551
0.577
0.4343
1.0343
-0.0341
-0.0119
-0.0425
-0.0836
-0.0161
-0.0046
0.0178
0.052
0.0502
-0.0138
0.0087
0.0037
0.0245
-0.0053
0.0055
-3.612
7.904
12.342
4
11.1198
-0.5912
-4.014
8.4946
-4.2164
14.9291
0.3532
0.4917
0.7252
-0.0442
-0.3706
-0.2576
-0.6065
0.1526
0.0174
-0.0488
-0.0177
-0.0229
0.0516
0.055
0.1119
-12.985
22.316
20.202
5
0.1515
-0.2602
0.1866
0.4749
-0.1736
1.0013
0.0044
-0.0093
-0.0251
-0.036
0.01
0.0171
-0.0454
-0.0202
-0.0144
-0.0326
-0.008
0.013
0.0125
-0.0007
0.0077
-2.334
8.489
49.911
6
0.4948
-0.4105
0.1142
0.7992
0.0054
0.3634
0.0194
-0.0158
0.0061
-0.0251
-0.0208
0.0678
-0.026
0.0002
0.0014
-0.0185
-0.0056
-0.0002
0.0092
-0.003
0.0102
-6.128
11.483
48.067
7
0.2931
-0.1025
0.3739
0.962
-0.0063
0.4937
-0.0351
0.0034
0.0016
0.092
-0.0256
-0.0323
0.0653
0.0364
0.0607
-0.0271
0.0031
0.004
0.0006
0.0034
0.0061
2.706
5.577
58.367
8
20.7865
-1.3255
12.3014
19.3299
11.8703
24.0291
-1.0734
0.1656
1.4363
-0.1931
0.4927
-0.5237
-0.9147
0.6013
0.5807
-0.0289
-0.0575
-0.0372
0.1053
0.0459
0.0675
11.991
16.874
40.747
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 128
2
X-RAY DIFFRACTION
2
A
129 - 160
3
X-RAY DIFFRACTION
3
A
161 - 207
4
X-RAY DIFFRACTION
4
A
208 - 214
5
X-RAY DIFFRACTION
5
B
3 - 81
6
X-RAY DIFFRACTION
6
B
82 - 157
7
X-RAY DIFFRACTION
7
B
158 - 199
8
X-RAY DIFFRACTION
8
B
200 - 208
+
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