L: Fab fragment 1D9 light chain H: Fab fragment 1D9 heavy chain A: Reticulon-4 receptor B: Fab fragment 1D9 light chain C: Fab fragment 1D9 heavy chain D: Reticulon-4 receptor hetero molecules
Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2004 Details: Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Resolution: 3.1→44.04 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.886 / SU B: 66.516 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.31775
1987
5 %
RANDOM
Rwork
0.25288
-
-
-
obs
0.25613
37475
99.21 %
-
all
-
39874
-
-
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: 16.692 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.22 Å2
0 Å2
0 Å2
2-
-
0.41 Å2
0 Å2
3-
-
-
-0.19 Å2
Refinement step
Cycle: LAST / Resolution: 3.1→44.04 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11049
0
97
0
11146
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.025
0.021
11476
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.509
1.961
15653
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
9.204
5
1439
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.3
23.559
472
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
23.5
15
1783
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.826
15
70
X-RAY DIFFRACTION
r_chiral_restr
0.152
0.2
1781
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
8684
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
1.825
1.5
7225
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.244
2
11652
X-RAY DIFFRACTION
r_scbond_it
4.352
3
4251
X-RAY DIFFRACTION
r_scangle_it
6.959
4.5
4001
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
Ens-ID
Number
Type
Rms dev position (Å)
Weight position
1
1120
TIGHTPOSITIONAL
0.07
0.05
1
1056
MEDIUMPOSITIONAL
0.07
0.5
1
1120
TIGHTTHERMAL
0.1
0.5
1
1056
MEDIUMTHERMAL
0.12
2
2
872
TIGHTPOSITIONAL
0.34
0.05
2
751
MEDIUMPOSITIONAL
0.5
0.5
2
872
TIGHTTHERMAL
0.71
0.5
2
751
MEDIUMTHERMAL
1.08
2
3
872
TIGHTPOSITIONAL
0.29
0.05
3
811
MEDIUMPOSITIONAL
0.49
0.5
3
872
TIGHTTHERMAL
0.95
0.5
3
811
MEDIUMTHERMAL
1.21
2
1
1120
TIGHTPOSITIONAL
0.07
0.05
1
872
TIGHTPOSITIONAL
0.34
0.05
1
872
TIGHTPOSITIONAL
0.29
0.05
1
1056
MEDIUMPOSITIONAL
0.07
0.5
1
751
MEDIUMPOSITIONAL
0.5
0.5
1
811
MEDIUMPOSITIONAL
0.49
0.5
1
1120
TIGHTTHERMAL
0.1
0.5
1
872
TIGHTTHERMAL
0.71
0.5
1
872
TIGHTTHERMAL
0.95
0.5
1
1056
MEDIUMTHERMAL
0.12
2
1
751
MEDIUMTHERMAL
1.08
2
1
811
MEDIUMTHERMAL
1.21
2
LS refinement shell
Resolution: 3.1→3.18 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.407
164
-
Rwork
0.369
2650
-
obs
-
-
98.15 %
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
1.8218
-1.5096
-2.4341
22.2449
0.3747
5.7545
0.6942
0.1257
0.0947
-0.5937
-0.5762
1.1899
-0.6021
-0.4925
-0.118
0.7193
0.0064
0.0379
1.0192
-0.0237
0.7994
96.35
35.533
32.413
2
5.0846
-0.4786
1.149
2.137
2.0424
7.4543
0.5944
0.2094
-0.0504
-0.2531
-0.6239
0.3125
-0.4593
-0.2146
0.0295
0.6445
0.0412
-0.0077
0.6163
-0.0656
0.5516
103.624
29.711
26.711
3
7.6457
-1.7445
3.7174
2.7055
-1.6026
5.8136
0.2047
0.4335
-0.0541
-0.2576
-0.0379
-0.153
0.1643
0.2747
-0.1668
0.6315
-0.1717
0.0011
0.4767
0.0152
0.5309
123.156
27.034
31.348
4
8.5354
-1.0288
2.7326
12.1264
0.8882
4.5901
0.0562
-0.2446
0.321
-0.4586
-0.1597
-0.6068
-0.057
0.506
0.1036
0.6655
-0.2492
-0.065
0.7301
0.0921
0.6876
137.987
25.987
43.909
5
2.9718
0.8376
1.4991
4.2557
-1.2879
5.0767
0.3362
-0.3418
-0.7773
0.1377
-0.4851
-0.8859
0.7314
0.4055
0.1489
0.9272
-0.0355
-0.1456
1.1315
0.1607
1.0419
144.447
17.426
54.651
6
8.7459
0.9338
2.9209
1.1064
-0.038
3.1214
0.3811
0.5792
-0.3462
0.2226
0.0556
-0.2163
0.3681
0.3075
-0.4367
0.7546
-0.0506
-0.1273
0.5562
-0.0089
0.7405
23.638
75.433
50.162
7
16.5791
6.1499
5.5973
3.016
5.2355
28.3657
0.8891
-0.5106
-0.7492
0.6967
-0.0175
0.1624
0.9804
-0.5146
-0.8716
0.7794
0.1358
0.0251
0.1638
0.28
1.0733
17.813
77.607
59.525
8
2.973
0.9013
1.3558
1.6382
0.4461
0.9677
0.5824
-0.3714
-0.5962
0.1461
-0.118
-0.0859
-0.0479
0.025
-0.4644
0.7167
-0.0005
0.0936
0.4012
-0.0348
0.632
7.262
78.418
41.489
9
1.0427
-1.9003
1.2831
6.7153
-0.55
9.0839
0.1133
0.7393
0.061
-0.3307
-0.3672
-0.4146
0.7377
0.3683
0.2538
0.5854
-0.0719
0.0145
1.0017
-0.0426
0.8484
-3.723
79.331
27.429
10
2.9425
-0.0472
2.3615
14.8902
-6.0046
9.9375
-0.0221
0.4709
-0.11
-0.7559
0.2489
0.1176
0.7242
-0.2589
-0.2269
0.8091
0.1183
0.0317
0.7613
-0.1591
0.8976
-14.462
80.927
20.645
11
4.7521
-0.7721
3.5457
3.4023
-3.5829
7.3078
-0.3847
0.4037
0.8636
0.0334
0.3489
-0.1533
-0.5373
-0.455
0.0358
0.7471
-0.1328
0.0312
0.5514
0.077
0.7943
19.188
98.044
49.169
12
9.6989
2.8763
-8.7076
4.5321
1.031
14.4624
-0.4354
0.5901
0.5508
0.1791
0.3717
-0.9362
0.2397
-0.5859
0.0637
0.9873
-0.0092
-0.1487
0.7986
-0.0133
1.3044
26.041
103.014
49.189
13
1.6414
-1.2729
0.9711
1.4777
-0.2495
3.7222
-0.0508
0.4564
-0.0729
-0.1626
0.0006
-0.0437
-0.3664
0.4077
0.0502
0.8201
-0.0663
0.0687
0.4428
0.0664
0.7541
9.023
92.913
42.453
14
4.0854
3.2293
-1.7211
2.8173
-2.7138
12.2637
-0.0711
0.0541
-0.1399
0.1899
0.0016
-0.2906
-0.3211
0.1101
0.0696
0.7194
0.1312
-0.0211
0.5168
-0.0235
0.7357
-5.437
92.804
38.693
15
8.6667
2.0719
-4.4327
3.4199
-1.4706
8.7714
0.1255
1.553
0.6884
0.0441
-0.0183
0.1188
-0.7193
-0.3396
-0.1072
0.7768
0.0542
-0.066
0.3691
0.0739
0.6656
-8.808
92.781
37.183
16
3.3928
-0.2536
0.1965
5.2734
1.732
7.6866
0.1612
-0.2035
0.2425
-0.0192
-0.0746
0.8472
-0.3983
-0.938
-0.0866
0.605
-0.0299
-0.0099
0.8216
-0.0233
0.606
29.045
93.677
73.441
17
7.2855
-1.6955
-0.3218
7.6859
-0.1054
2.6669
0.209
-0.0744
-0.1418
-0.3043
-0.2376
0.3137
-0.0632
-0.4217
0.0287
0.6173
-0.1144
-0.0575
0.7457
-0.0187
0.4812
40.635
90.537
72.015
18
8.7296
-1.955
3.2416
3.0837
-1.3327
4.7311
0.0733
0.258
0.1383
-0.2851
-0.1291
-0.4014
0.0174
0.2028
0.0557
0.6172
-0.2584
-0.0401
0.6096
-0.0035
0.5592
55.168
89.649
78.639
19
8.0888
-0.9118
2.9909
7.791
0.2179
3.6911
0.3399
-0.2502
0.324
-0.162
-0.3413
-0.7511
-0.1087
0.889
0.0013
0.7037
-0.2089
-0.0976
0.8821
0.0632
0.7057
67.044
87.957
88.587
20
7.8117
-2.9763
1.2543
7.9728
0.4045
2.454
0.2018
-0.9713
-0.2979
0.0916
-0.082
-0.9842
0.7771
0.1472
-0.1198
0.9925
-0.2332
-0.1812
1.4085
0.1824
0.9285
72.876
79.718
99.692
21
3.8123
-0.7389
2.089
5.8613
-2.6463
3.3396
-0.2139
0.6856
0.3684
-0.2022
0.1735
-0.0421
-0.5843
-0.1334
0.0404
0.7735
-0.0362
-0.0054
0.6062
0.0089
0.7333
90.848
35.36
4.135
22
1.6909
-0.1151
2.6825
4.4207
-1.6494
7.5442
-0.4688
0.1351
0.6678
-0.3451
0.214
-0.5309
-0.5962
1.0982
0.2548
0.7503
-0.0436
0.101
0.7643
-0.0202
1.0253
94.882
35.711
3.158
23
3.6571
-0.4658
1.0004
1.422
-1.2644
3.9494
-0.0584
0.6265
-0.2527
-0.2341
0.1444
0.0871
-0.2278
-0.4075
-0.0859
0.853
0.1827
0.0193
0.4191
-0.0525
0.6553
68.907
29.249
-8.726
24
6.7937
3.1749
-0.169
8.1423
-0.0832
1.1348
0.2522
0.0612
-0.5073
0.1158
-0.4472
-0.5125
-0.2937
0.8813
0.195
0.7233
0.0227
-0.1024
0.8472
0.0123
0.6436
69.195
28.339
-8.537
25
5.2787
1.1204
-3.9421
7.946
0.0021
4.995
0.0121
0.958
0.6459
0.4492
0.1441
0.2525
-0.8757
-0.7552
-0.1561
0.8851
0.1274
-0.0882
0.4831
0.0792
0.5692
57.955
30.373
-5.458
26
7.376
0.455
4.4721
1.9214
0.9045
4.1115
0.6218
-0.1983
-0.9096
0.1188
-0.0499
-0.2238
0.6474
-0.097
-0.5719
0.8056
0.0754
-0.17
0.6351
-0.0328
0.8055
94.214
13.658
6.931
27
5.5363
0.6415
2.7336
0.544
0.2382
2.55
0.5007
-0.2704
-0.9151
0.1495
0.0431
-0.1336
0.3063
-0.1296
-0.5438
0.7975
0.0859
-0.0276
0.6738
-0.0813
0.7472
78.743
14.999
-2.776
28
7.6676
-4.354
7.3489
8.8234
-3.7152
7.6046
0.4038
0.3888
-0.1619
-1.0283
-0.5822
0.1542
0.8239
0.0221
0.1783
0.9494
0.2009
0.0787
1.4356
-0.2124
0.9471
65.128
15.243
-25.418
29
2.4439
-1.7321
4.7398
10.5678
-4.5064
14.009
0.5819
0.5333
0.0375
-0.5317
-0.4628
0.4635
0.609
0.6611
-0.1191
0.5382
0.0454
0.0512
0.7697
-0.0668
0.732
64.758
20.124
-17.984
30
5.5598
-0.8878
3.5429
6.0615
-6.7479
9.1509
0.3347
-0.3527
-1.3512
-0.3997
1.122
1.0538
1.0154
-1.1219
-1.4567
1.0382
0.1057
-0.1665
1.4791
-0.2565
1.1387
57.058
12.462
-21.178
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
26 - 45
2
X-RAY DIFFRACTION
2
A
46 - 92
3
X-RAY DIFFRACTION
3
A
93 - 213
4
X-RAY DIFFRACTION
4
A
214 - 257
5
X-RAY DIFFRACTION
5
A
258 - 309
6
X-RAY DIFFRACTION
6
B
2 - 49
7
X-RAY DIFFRACTION
7
B
50 - 67
8
X-RAY DIFFRACTION
8
B
68 - 146
9
X-RAY DIFFRACTION
9
B
147 - 186
10
X-RAY DIFFRACTION
10
B
187 - 219
11
X-RAY DIFFRACTION
11
C
1 - 54
12
X-RAY DIFFRACTION
12
C
55 - 82
13
X-RAY DIFFRACTION
13
C
83 - 142
14
X-RAY DIFFRACTION
14
C
143 - 169
15
X-RAY DIFFRACTION
15
C
170 - 220
16
X-RAY DIFFRACTION
16
D
26 - 79
17
X-RAY DIFFRACTION
17
D
80 - 125
18
X-RAY DIFFRACTION
18
D
126 - 212
19
X-RAY DIFFRACTION
19
D
213 - 255
20
X-RAY DIFFRACTION
20
D
256 - 309
21
X-RAY DIFFRACTION
21
H
1 - 57
22
X-RAY DIFFRACTION
22
H
58 - 106
23
X-RAY DIFFRACTION
23
H
107 - 153
24
X-RAY DIFFRACTION
24
H
154 - 184
25
X-RAY DIFFRACTION
25
H
185 - 220
26
X-RAY DIFFRACTION
26
L
1 - 63
27
X-RAY DIFFRACTION
27
L
64 - 146
28
X-RAY DIFFRACTION
28
L
147 - 165
29
X-RAY DIFFRACTION
29
L
166 - 196
30
X-RAY DIFFRACTION
30
L
197 - 219
+
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