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 E: C-type lectin domain family 4 member K F: C-type lectin domain family 4 member K hetero molecules
Resolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.2 / Num. unique all: 6800 / % possible all: 99.1
-
Processing
Software
Name
Version
Classification
Blu-Ice
ice
datacollection
COMO
phasing
PHENIX
(phenix.refine: 1.5_2)
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: a model from a low resolution data set. Resolution: 2.3→47.958 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2385
2380
5.08 %
shells
Rwork
0.1821
-
-
-
obs
0.1849
46871
99.42 %
-
all
-
46871
-
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.75 Å2 / ksol: 0.319 e/Å3
Refinement step
Cycle: LAST / Resolution: 2.3→47.958 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7795
0
6
407
8208
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
8122
X-RAY DIFFRACTION
f_angle_d
0.818
10947
X-RAY DIFFRACTION
f_dihedral_angle_d
17.077
2849
X-RAY DIFFRACTION
f_chiral_restr
0.057
1121
X-RAY DIFFRACTION
f_plane_restr
0.003
1398
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.3-2.347
0.2951
119
0.23
2543
X-RAY DIFFRACTION
98
2.347-2.398
0.333
119
0.2389
2633
X-RAY DIFFRACTION
99
2.398-2.4538
0.3046
156
0.2332
2605
X-RAY DIFFRACTION
99
2.4538-2.5151
0.3191
201
0.2195
2502
X-RAY DIFFRACTION
99
2.5151-2.5831
0.2845
119
0.2098
2617
X-RAY DIFFRACTION
99
2.5831-2.6591
0.2847
119
0.2052
2617
X-RAY DIFFRACTION
100
2.6591-2.7449
0.286
119
0.2039
2635
X-RAY DIFFRACTION
99
2.7449-2.843
0.27
119
0.2087
2625
X-RAY DIFFRACTION
99
2.843-2.9569
0.3015
179
0.2095
2578
X-RAY DIFFRACTION
99
2.9569-3.0914
0.2692
178
0.2037
2591
X-RAY DIFFRACTION
100
3.0914-3.2544
0.2536
119
0.1941
2610
X-RAY DIFFRACTION
100
3.2544-3.4582
0.2625
119
0.1864
2642
X-RAY DIFFRACTION
100
3.4582-3.7251
0.242
119
0.1642
2667
X-RAY DIFFRACTION
100
3.7251-4.0998
0.2167
119
0.1573
2668
X-RAY DIFFRACTION
100
4.0998-4.6926
0.1695
238
0.1347
2531
X-RAY DIFFRACTION
100
4.6926-5.9105
0.1965
119
0.151
2682
X-RAY DIFFRACTION
100
5.9105-47.9687
0.1695
119
0.1571
2745
X-RAY DIFFRACTION
100
Refinement TLS params.
Refine-ID: X-RAY DIFFRACTION
ID
Method
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
refined
0.8036
-0.0902
-0.2025
1.547
0.2381
0.67
-0.0025
-0.0375
-0.0069
0.1896
0.0879
-0.1504
0.1065
0.0548
-0.0638
0.241
-0.004
-0.03
0.1288
-0.0394
0.1777
2.5803
62.4017
104.2724
2
0.2076
0.0167
0.4133
2.1299
2.5425
2.6654
-0.0376
0.096
-0.0563
0.4392
-0.0765
0.4235
0.6572
0.0812
0.1189
0.4961
-0.0092
0.0494
0.2303
-0.054
0.301
3
1.1787
-0.6623
-0.8516
0.9474
1.121
2.282
-0.0327
0.0664
-0.0198
0.0915
-0.0507
0.0423
0.0109
-0.0396
0.0535
0.2123
-0.0162
0.0223
0.1011
0.0043
0.1017
4
0.7638
-0.6055
0.5365
0.7098
-0.2251
0.8318
0.0487
0.0926
-0.2877
-0.1147
-0.0923
0.5887
-0.223
-0.1685
0.0632
0.1781
-0.0476
-0.0076
0.2377
-0.083
0.3544
5
0.8151
0.156
-0.8404
1.5041
-0.3137
0.4833
0.0338
0.2117
0.0184
0.0233
-0.0125
-0.0545
0.1258
-0.1361
-0.0018
0.2942
-0.0292
-0.0117
0.1614
0.0183
0.1017
6
1.6924
0.0841
1.1922
0.3173
0.1339
1.3794
0.2991
0.3009
-0.2479
0.1381
-0.1075
-0.0373
0.3577
0.1649
-0.1502
0.3817
0.001
-0.059
0.2005
-0.043
0.2274
7
1.2933
0.524
-0.7212
0.9155
-0.2689
1.4225
0.0688
-0.0875
-0
-0.052
-0.1375
0.011
-0.1432
0.202
-0.0168
0.2356
-0.0142
0.0373
0.1794
0.0274
0.0978
8
2.2794
0.3044
0.0845
3.7015
-0.0851
0.0268
0.0162
-0.4859
0.0813
0.881
-0.488
-0.0226
-0.0211
-0.4272
0.2666
0.3852
-0.1342
0.0493
0.4728
-0.0245
0.2026
9
2.4982
-0.8612
1.5746
1.1229
-0.9842
1.6078
-0.0077
-0.2077
-0.1673
-0.2146
-0.02
0.2934
-0.1572
-0.2687
0.0169
0.2534
0.0493
-0.0295
0.2767
-0.034
0.2761
10
0.0072
-0.1241
-0.2616
0.1691
-0.3602
5.4239
0.1742
0.0306
0.0509
-0.0758
0.4404
0.2263
-0.11
-1.5095
-0.4369
0.2046
0.0578
0.1145
0.5678
0.1503
0.2898
11
1.9253
-0.2483
-0.96
0.974
0.535
1.7301
0.2056
0.0601
-0.5522
-0.108
-0.1923
0.3405
0.0618
-0.1163
-0.0459
0.224
0.0161
-0.0847
0.1032
-0.0004
0.3336
12
1.9419
1.1246
0.097
0.8614
0.2565
0.1759
0.3968
-0.9146
-0.3511
0.3696
-0.578
-0.1444
0.0001
0.0756
-0.1499
0.4669
-0.1787
0.0004
0.654
0.1187
0.3096
Refinement TLS group
Selection details: chain F and resid 165:198
+
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