A: C-type lectin domain family 4 member K B: C-type lectin domain family 4 member K C: C-type lectin domain family 4 member K D: C-type lectin domain family 4 member K hetero molecules
Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.666 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22863
1280
5.1 %
RANDOM
Rwork
0.18077
-
-
-
obs
0.18318
23863
98.5 %
-
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: 27.571 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.07 Å2
0 Å2
0 Å2
2-
-
-0.07 Å2
0 Å2
3-
-
-
0.13 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4273
0
96
204
4573
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.012
0.022
4551
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.36
1.946
6217
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.644
5
521
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.564
24.22
218
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.42
15
663
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.351
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
629
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
3532
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
0.547
1.5
2618
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.091
2.5
4222
X-RAY DIFFRACTION
r_scbond_it
2.435
3.5
1933
X-RAY DIFFRACTION
r_scangle_it
4.027
10
1995
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.334
97
-
Rwork
0.278
1753
-
obs
-
-
97.57 %
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
3.6554
-0.5417
-1.3019
2.7975
-0.4246
5.1057
-0.0183
0.0282
-0.0819
-0.2329
-0.0538
0.1008
0.0861
0.0279
0.072
0.0873
0.0151
-0.0889
0.0437
-0.0191
0.1067
6.9527
15.7419
-34.1143
2
3.6218
0.2702
0.6238
1.7349
-0.2495
2.5099
-0.0747
0.1656
0.4572
-0.279
-0.0113
0.2377
-0.3018
0.0035
0.0859
0.1527
0.0255
-0.0969
0.0974
-0.0152
0.1721
5.2263
25.8021
-33.9579
3
17.0552
15.138
3.6539
13.441
3.2419
0.7845
1.2818
-0.1164
-3.0979
1.3081
-0.3841
-2.7333
0.3572
-0.0145
-0.8977
0.8217
0.2753
-0.3902
0.5786
-0.1578
0.6195
28.9473
4.4137
-28.8688
4
3.6458
0.0422
0.707
4.0019
-0.1453
3.0312
0.0441
0.1132
0.1118
-0.1574
-0.1734
-0.0377
-0.0177
0.0795
0.1294
0.0666
0.0065
0.0059
0.0846
0.0125
0.0084
31.3979
26.0397
-31.7639
5
3.904
0.8011
0.7246
3.1993
0.4165
9.4394
-0.0635
0.3028
-0.2364
-0.3546
-0.0428
-0.2404
0.3342
0.347
0.1063
0.0841
0.0171
0.071
0.1183
-0.0064
0.1625
37.3063
14.6543
-36.0788
6
1.8529
2.064
-0.5364
3.0925
-2.0689
3.8913
0.002
0.0094
0.0405
0.0236
-0.0884
-0.1374
-0.1629
0.105
0.0864
0.0395
-0.043
0.0357
0.1304
0.0182
0.1004
34.0409
26.5056
-30.1649
7
4.0052
0.5571
-0.3932
1.6429
-0.5708
4.3194
-0.0656
-0.1542
-0.063
0.1538
0.0062
-0.0807
0.1812
0.0392
0.0595
0.0697
0.0057
-0.0181
0.0301
0.0192
0.0486
31.6325
15.0901
-5.4249
8
12.3601
-3.4878
0.9739
11.762
3.6238
1.4955
-0.0352
-0.3359
1.3109
-0.3442
-0.2131
-0.095
-0.1697
-0.1826
0.2483
0.1739
0.075
-0.0375
0.1641
-0.0317
0.1786
23.9907
28.7099
-7.3616
9
5.1151
-0.0653
0.8733
2.0223
0.1362
3.0044
-0.0146
-0.1526
0.6789
0.1261
-0.0194
-0.1296
-0.1594
-0.0243
0.034
0.0901
0.0125
-0.0393
0.0699
-0.002
0.124
33.4411
23.2202
-5.5366
10
3.0061
-0.5758
-0.0625
4.4266
1.6852
4.427
-0.0083
-0.316
0.2028
0.1408
-0.1892
0.2059
-0.2899
-0.0569
0.1975
0.0801
0.0006
0.0413
0.0918
-0.0024
0.0851
4.2684
27.4661
-5.9155
11
8.0647
0.5212
2.6191
7.2897
-2.1829
5.2389
0.1788
0.2895
-0.5982
-0.4509
-0.1111
-0.12
0.6705
0.3653
-0.0677
0.1352
0.0207
0.0268
0.1069
0.0282
0.1027
11.5382
13.279
-11.2686
12
3.118
-0.6943
-0.596
4.6599
0.1647
4.7352
-0.0954
-0.2232
-0.4438
0.3677
-0.08
0.3183
0.3972
-0.115
0.1754
0.0945
-0.0008
0.0784
0.1368
0.0213
0.1577
2.431
16.7786
-6.0426
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
198 - 262
2
X-RAY DIFFRACTION
2
A
263 - 322
3
X-RAY DIFFRACTION
3
A
323 - 332
4
X-RAY DIFFRACTION
4
B
196 - 275
5
X-RAY DIFFRACTION
5
B
276 - 305
6
X-RAY DIFFRACTION
6
B
306 - 325
7
X-RAY DIFFRACTION
7
C
198 - 259
8
X-RAY DIFFRACTION
8
C
260 - 279
9
X-RAY DIFFRACTION
9
C
280 - 331
10
X-RAY DIFFRACTION
10
D
196 - 253
11
X-RAY DIFFRACTION
11
D
254 - 275
12
X-RAY DIFFRACTION
12
D
276 - 325
+
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