Resolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.58 / % possible all: 87.8
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
HKL-2000
datareduction
REFMAC
5.2.0005
refinement
HKL-3000
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
HKL-3000
phasing
DM
phasing
MLPHARE
phasing
SHELXD
phasing
SHELXE
modelbuilding
O
modelbuilding
CCP4
phasing
SOLVE
phasing
RESOLVE
phasing
ARP/wARP
modelbuilding
SHARP
phasing
autoSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.1→28.41 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.67 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.215 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS 1.1, O, COOT programs were also used during refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
1172
5.1 %
RANDOM
Rwork
0.187
-
-
-
all
0.19
22944
-
-
obs
0.19
22944
-
-
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: 26.58 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.48 Å2
-0.74 Å2
0 Å2
2-
-
-1.48 Å2
0 Å2
3-
-
-
2.22 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→28.41 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2793
0
0
124
2917
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.022
2845
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2614
X-RAY DIFFRACTION
r_angle_refined_deg
1.805
1.959
3846
X-RAY DIFFRACTION
r_angle_other_deg
0.926
3
6049
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.57
5
349
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.268
24.101
139
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.664
15
496
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.635
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.105
0.2
435
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
3159
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
575
X-RAY DIFFRACTION
r_nbd_refined
0.227
0.2
682
X-RAY DIFFRACTION
r_nbd_other
0.191
0.2
2628
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
1388
X-RAY DIFFRACTION
r_nbtor_other
0.093
0.2
1632
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.191
0.2
135
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
0.45
0.2
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.343
0.2
28
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.195
0.2
3
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
1.332
1.5
1937
X-RAY DIFFRACTION
r_mcbond_other
0.308
1.5
706
X-RAY DIFFRACTION
r_mcangle_it
1.624
2
2816
X-RAY DIFFRACTION
r_scbond_it
3.08
3
1162
X-RAY DIFFRACTION
r_scangle_it
4.322
4.5
1030
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.1→2.15 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.268
92
-
Rwork
0.184
1601
-
obs
-
-
99.59 %
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
6.2316
-0.1708
-7.6997
0.9425
-0.6054
11.1313
-0.001
0.4678
-0.2768
-0.2765
-0.068
0.1052
-0.1819
-0.2997
0.069
0.0293
-0.0653
-0.0102
0.1376
-0.1161
0.0659
16.511
-9.519
47.125
2
9.0838
-0.7384
-2.5721
24.5414
4.0539
9.8298
0.3857
-0.2392
0.2737
-0.2216
-0.2038
1.1135
0.1227
0.0416
-0.1818
-0.0158
0.0021
0.0002
0.1267
-0.0715
0.1201
4.879
-7.343
63.647
3
3.1476
1.4276
0.826
2.2794
0.4841
1.5753
-0.1419
-0.2898
-0.065
0.0929
0.0274
-0.1465
0.0797
0.0233
0.1146
0.0272
0.0169
0.0067
0.1242
-0.0256
0.0665
30.064
-5.017
63.231
4
7.5895
3.8679
2.0787
2.5216
0.2459
1.9075
0.2704
-0.2339
-0.9846
0.1661
-0.1084
-0.2892
0.2601
-0.2621
-0.162
0.0191
-0.0399
0.0191
0.0546
-0.0275
0.0932
19.535
-16.235
54.905
5
6.7422
2.2665
-2.346
1.9879
-0.876
7.6257
0.0143
-0.3237
-0.5837
0.0004
-0.2977
-0.0755
0.8624
0.0797
0.2834
0.0924
-0.0126
0.1196
-0.0223
-0.0479
0.146
27.434
-18.153
46.442
6
12.8004
-2.6987
-3.2988
2.5142
0.0564
2.6579
-0.192
-0.3491
-0.5865
0.1484
-0.0007
0.2208
0.0425
0.0651
0.1927
0.0776
-0.0292
0.0229
0.1352
-0.0221
0.0505
18.538
-10.264
68.349
7
4.7394
1.7242
-1.3635
6.5009
-2.2066
1.0522
0.0189
-0.9729
-0.1207
0.4377
-0.1265
0.2566
0.0405
-0.1848
0.1076
0.0661
-0.0349
0.0035
0.2221
-0.0321
-0.0881
23.792
-7.861
74.813
8
3.9441
-1.0209
1.4797
2.4883
-0.7846
1.5955
-0.0321
-0.3024
0.1399
0.1487
0.0447
0.2587
-0.0353
-0.2562
-0.0127
-0.0063
0.021
0.0454
0.1341
-0.0911
0.1089
15.594
5.376
57.283
9
2.7883
-1.1952
-0.6821
1.7038
0.613
2.3636
-0.0734
0.0014
0.1125
-0.0703
0.0277
-0.0971
-0.0728
0.0153
0.0457
0.0471
-0.0259
0.0062
0.0999
-0.0397
0.1023
29.882
2.723
49.423
10
4.2725
-3.3691
1.4003
14.6285
-22.7863
39.7273
-0.4996
0.113
1.1932
0.417
-0.3123
-0.9484
-1.1866
-1.2353
0.8119
0.0694
0.0714
-0.1672
-0.0845
-0.0766
0.1647
23.988
19.039
57.646
11
1.3795
0.7399
0.6312
1.0548
0.4157
3.3852
-0.0948
-0.0953
0.2358
0.1714
-0.1358
-0.1842
-0.3312
-0.1445
0.2306
0.0442
0.0104
-0.068
0.0675
-0.0515
0.108
32.7
8.992
57.518
12
8.1292
3.0581
2.3938
3.1042
0.4791
0.7958
0.1238
0.0364
-0.1395
-0.4694
0.0248
0.3222
0.1833
0.0804
-0.1485
0.0787
0.0232
-0.0249
0.1101
-0.0617
0.021
16.875
3.24
39.894
13
9.8064
0.1307
-0.1864
2.932
-0.7063
1.8128
0.2784
1.1445
0.6666
-0.2874
-0.0911
0.3303
-0.0998
-0.2453
-0.1873
0.0616
0.0353
-0.0637
0.0356
0.0211
0.0249
16.525
9.017
36.451
14
16.0985
5.1654
-1.9653
7.9017
-2.024
2.5277
-0.0214
0.4348
0.0937
-0.5996
-0.2114
0.7052
0.0549
-0.4593
0.2328
0.0841
0.0102
0.0109
0.1598
-0.1228
-0.0515
25.731
-2.274
34.784
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
2 - 20
4 - 22
2
X-RAY DIFFRACTION
2
A
A
21 - 27
23 - 29
3
X-RAY DIFFRACTION
3
A
A
28 - 62
30 - 64
4
X-RAY DIFFRACTION
4
A
A
63 - 92
65 - 94
5
X-RAY DIFFRACTION
5
A
A
93 - 124
95 - 126
6
X-RAY DIFFRACTION
6
A
A
125 - 160
127 - 162
7
X-RAY DIFFRACTION
7
A
A
161 - 187
163 - 189
8
X-RAY DIFFRACTION
8
B
B
2 - 35
4 - 37
9
X-RAY DIFFRACTION
9
B
B
36 - 79
38 - 81
10
X-RAY DIFFRACTION
10
B
B
80 - 104
82 - 106
11
X-RAY DIFFRACTION
11
B
B
105 - 138
107 - 140
12
X-RAY DIFFRACTION
12
B
B
139 - 147
141 - 149
13
X-RAY DIFFRACTION
13
B
B
148 - 172
150 - 174
14
X-RAY DIFFRACTION
14
B
B
173 - 187
175 - 189
+
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