Kinesin-likeproteinKIF1A / Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A- ...Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A-related protein / hUnc-104
Mass: 20964.643 Da / Num. of mol.: 4 / Fragment: CC1-FHA tandem, UNP residues 430-607 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KIF1A, ATSV, C2orf20 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q12756
Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.86 / SU B: 24.207 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 1.174 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28257
1286
5.1 %
RANDOM
Rwork
0.25168
-
-
-
obs
0.25325
24084
96.36 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 39.229 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.48 Å2
0 Å2
0 Å2
2-
-
1.89 Å2
0 Å2
3-
-
-
-2.37 Å2
Refinement step
Cycle: LAST / Resolution: 2.51→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5405
0
26
160
5591
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.021
5510
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.267
1.97
7416
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.138
5
699
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.713
23.574
249
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.817
15
960
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.643
15
50
X-RAY DIFFRACTION
r_chiral_restr
0.078
0.2
831
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
4130
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.231
0.2
2292
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.309
0.2
3615
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.175
0.2
250
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
0.243
0.2
167
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.222
0.2
15
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
0.537
1.5
3579
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.67
2
5583
X-RAY DIFFRACTION
r_scbond_it
1.076
3
2118
X-RAY DIFFRACTION
r_scangle_it
1.633
4.5
1833
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.511→2.576 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.402
89
-
Rwork
0.305
1500
-
obs
-
-
83.11 %
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
1.8925
1.0224
-0.156
2.9837
1.1054
9.763
0.2582
0.298
-0.2037
-0.5097
-0.2431
-0.2226
0.6988
0.1337
-0.015
-0.0169
0.0462
0.0561
0.0933
-0.0297
0.0541
-7.823
-17.7202
-70.0754
2
7.2192
3.9049
4.4793
2.1122
2.4229
2.7792
0.1739
-0.3633
0.143
0.1473
-0.1102
-0.1739
0.2278
0.0691
-0.0637
0.0694
-0.0323
0.0299
0.2181
0.0004
0.1502
4.5293
-5.8821
-47.0574
3
4.0857
0.6119
-2.2475
1.8903
3.0179
15.7147
0.1766
-0.2891
-0.3045
0.0359
-0.0828
0.4422
0.3751
0.5308
-0.0938
-0.0383
0.0007
-0.0131
0.1207
-0.1075
0.1175
12.1563
2.7846
-26.8255
4
8.1285
2.7922
4.0087
3.1845
0.2708
3.376
-0.5492
0.1336
-0.5235
-0.5747
0.1708
0.4151
-0.0101
-0.4202
0.3785
0.1
0.0151
-0.0339
0.1527
-0.0611
0.1179
11.7895
2.0333
-18.1848
5
1.3267
0.7366
-0.9856
0.4089
-0.5387
3.984
0.0881
-0.2142
0.1593
-0.1806
-0.0356
0.1158
-0.0961
-0.1892
-0.0525
0.0128
-0.0047
-0.0304
0.0602
-0.0182
0.0989
16.8645
15.7663
-11.8173
6
7.1928
-3.6083
-4.831
22.3866
1.2728
3.309
0.2522
1.0611
0.7524
-0.316
-0.8825
-0.4278
-1.2944
0.2186
0.6303
0.2088
-0.0085
-0.0971
0.1229
0.0096
0.0857
24.9245
28.6197
-14.9749
7
2.7621
-0.9984
-0.1723
1.7515
0.1741
1.3999
0.1543
0.2618
-0.0643
-0.1293
-0.041
-0.081
0.0882
0.3336
-0.1133
0.0422
0.004
0.0127
0.1203
-0.0082
0.0323
27.1651
20.1073
-11.1386
8
2.1121
-2.1473
-0.1309
2.6145
-0.6189
1.3187
-0.056
-0.2802
0.0297
0.1743
0.08
-0.3088
-0.1258
0.2298
-0.0239
0.0161
-0.042
0.0082
0.1069
-0.0135
0.0507
28.8085
17.518
-0.3992
9
4.5689
-7.0378
-1.6448
12.0779
2.4905
0.5937
-0.0261
-0.0572
-0.0807
0.1034
-0.0425
0.3631
0.1054
-0.2382
0.0686
0.0173
-0.0045
0.0073
0.1231
0.042
0.0928
19.4121
15.2787
-3.1777
10
0.6373
2.0454
-0.8659
47.642
-10.4307
2.6019
0.219
-1.0677
-0.5062
0.2099
0.4448
-0.4808
0.2962
-1.5922
-0.6639
0.1588
0.0014
-0.0656
0.126
0.1041
-0.0463
25.3886
-1.5575
-4.5729
11
9.1266
4.9704
4.5392
7.5693
4.2937
7.1977
-0.1007
0.3972
-0.1807
0.0405
0.3442
0.0558
0.0157
0.2569
-0.2435
-0.0358
0.0606
-0.0005
0.0459
0.0436
0.0787
-20.1818
-13.8363
-61.8476
12
10.1107
6.0235
6.6745
8.2487
7.2832
6.7526
-0.4594
-0.5292
1.0227
0.7512
-0.1767
0.5924
-0.69
0.0059
0.6361
0.2177
-0.141
-0.0197
0.0444
0.0499
0.0127
-4.8193
-0.9362
-45.6561
13
1.1841
-1.8063
-0.425
2.7554
0.6483
0.1526
0.0416
0.7738
1.4956
0.4145
-0.123
1.0666
0.5273
0.1682
0.0814
0.2022
-0.1025
-0.1103
0.1746
-0.0818
0.1918
8.6427
10.9335
-29.4609
14
9.7045
4.0002
-4.8685
2.3984
-0.5523
5.2651
0.0119
1.2298
0.7043
-0.1063
0.1225
0.0616
0.1024
-0.4444
-0.1345
-0.0164
0.0208
-0.052
0.0574
-0.0303
0.0694
20.4717
15.8247
-20.4082
15
3.3502
-1.6601
1.2468
6.0218
0.7748
14.0256
0.4515
0.5262
0.2466
-0.4227
-0.5625
0.0106
0.5179
0.8904
0.111
-0.0224
-0.1029
0.0114
0.1293
-0.0409
0.0863
4.9418
11.078
-11.5538
16
5.6662
1.7293
-0.3515
2.8662
-1.488
0.8371
0.0939
-2.1173
-0.8743
0.3393
0.0872
0.0099
0.6397
-0.1462
-0.1811
0.3982
-0.0921
-0.2676
0.2219
-0.1377
0.3332
11.6551
1.0927
-9.032
17
4.981
-0.6723
0.3113
3.8224
-1.4742
4.625
-0.0625
0.331
-0.4994
-0.4279
0.1488
-0.0166
0.4604
-0.1806
-0.0863
0.0125
0.0137
-0.0249
0.0477
-0.1098
0.0018
-2.48
-0.2469
-16.2369
18
2.7789
-0.7978
1.1209
3.9775
-0.3932
3.6086
-0.0851
0.057
-0.1902
-0.0275
0.2792
0.4119
0.0902
-0.4866
-0.1941
-0.0287
-0.0382
-0.0338
0.0885
-0.0279
0.066
-8.4226
4.5311
-10.3941
19
6.8642
1.786
-0.8199
4.8146
0.6348
4.4894
-0.1092
-0.5498
-0.0943
-0.367
0.1291
0.2401
0.3375
0.0572
-0.0199
-0.0418
0.0414
-0.0063
0.0101
-0.0171
0.0875
-8.4872
10.6952
-4.7618
20
4.1215
-1.4844
1.235
8.8977
-5.2337
5.3849
-0.1341
0.1479
0.2314
0.029
0.0818
0.0667
-0.359
-0.0904
0.0523
0.0724
0.0155
-0.0238
0.0997
-0.0394
0.0452
-0.7669
13.6162
-9.4356
21
2.0941
-2.2551
-0.84
5.3569
-1.4258
5.4257
0.1289
0.15
0.3431
-0.428
0.0055
-0.3704
-0.2003
0.1962
-0.1344
-0.0135
0.0479
-0.0109
0.0607
0.0202
0.1325
30.7302
-28.5354
-49.6175
22
2.2826
0.5224
-2.4651
2.746
3.954
10.4349
0.67
-0.3316
0.5179
0.3473
-0.2237
0.0185
-1.0956
-0.2852
-0.4463
0.1676
0.034
0.0388
0.0679
-0.0363
0.0743
20.163
-16.9343
-24.4096
23
6.6658
2.9148
7.2389
4.1159
-1.8191
16.6055
0.7974
0.6866
-0.5482
-0.7236
-1.1206
-0.9158
-0.2106
0.2054
0.3232
0.1963
0.0024
0.1177
0.0948
0.084
-0.0265
16.5859
-12.7308
-1.6435
24
2.5513
1.3364
-2.8273
0.7
-1.4809
3.133
-0.1651
0.1627
0.0327
0.5499
0.1356
-0.6422
1.0844
0.7768
0.0295
0.258
-0.0196
0.0105
0.1214
-0.0009
-0.025
18.0407
-10.9542
7.0857
25
0.6263
-1.2831
1.5661
7.1686
-3.8459
4.0057
0.2881
-0.1876
0.0596
0.312
0.259
0.5458
0.6127
-0.5886
-0.5471
0.047
-0.0684
0.031
0.0653
-0.0881
0.0735
5.018
-8.0138
14.779
26
2.1268
3.077
0.2122
4.7973
1.6517
5.2534
0.1416
0.1529
0.0273
-0.2909
-0.0401
-0.1418
-0.5759
-0.0682
-0.1015
0.0146
0.0041
-0.0158
0.102
0.0458
-0.0107
7.5892
2.626
11.1086
27
7.1977
-2.2783
-1.6914
1.8432
-2.375
7.9467
0.0935
-0.0304
-0.2805
0.0206
-0.0656
0.3763
0.2749
-0.5263
-0.0279
0.0145
0.0844
0.0202
-0.0108
0.0025
0.1052
-2.6834
4.159
15.57
28
10.0955
1.9976
-5.4004
4.3472
-0.3177
4.0697
-0.1152
-0.0664
-0.1719
0.0823
0.0703
-0.3054
-0.2771
0.0391
0.0449
0.0405
0.0617
-0.0373
0.0095
0.0034
-0.0033
9.3479
8.8859
20.2646
29
2.8088
0.1197
0.3319
3.4201
-0.0541
2.5135
-0.1055
-0.0907
0.0104
0.4862
0.0239
0.2627
0.2314
-0.112
0.0816
0.1781
0.0365
-0.0019
0.1593
-0.0099
-0.0328
7.0755
2.612
25.5077
30
16.6906
-0.2524
1.9558
2.9559
0.6896
0.563
-0.2176
-0.7032
-0.1988
0.2496
0.0799
-0.7495
-0.1015
0.1364
0.1378
0.0709
0.012
-0.0252
0.0649
0.0086
0.0692
17.698
0.4891
19.7554
31
22.3981
-0.6067
-9.0912
8.8552
6.2806
7.8098
-0.4375
-0.2345
-1.1008
0.91
0.0355
-0.2946
1.5377
0.7587
0.402
-0.001
0.1521
-0.1295
0.1443
0.1301
0.1047
39.2456
-40.7847
-42.5104
32
5.368
-6.3798
-7.3917
9.4758
9.3603
14.4127
-0.3855
-0.1871
-0.2324
0.6709
0.0374
0.1156
0.6995
-0.2203
0.3481
0.0175
-0.0095
-0.0502
0.1084
0.0826
0.0828
26.2576
-30.6989
-27.6593
33
2.534
-2.3511
-2.4219
2.1833
2.2011
3.3787
-0.3123
0.3389
0.0607
0.0195
0.0691
0.2946
0.4327
-0.2267
0.2432
0.144
0.0186
0.0503
0.1416
-0.0641
0.0711
9.4644
-13.1078
-5.3593
34
1.1204
1.4115
0.3805
3.9895
-0.5715
0.6286
0.0699
0.1002
0.0047
-0.412
-0.0198
0.1763
0.1201
-0.1299
-0.0502
0.1446
0.0366
0.0345
0.0636
-0.049
-0.0125
7.8382
-12.2713
9.3367
35
19.6586
-7.2445
-9.9828
2.6697
3.6788
5.0693
0.679
0.6325
0.2297
0.5318
-0.2812
-1.0782
0.1337
2.2127
-0.3978
0.219
-0.2021
0.1365
0.0378
0.0818
0.2332
20.5394
-12.1142
15.8611
36
1.1337
0.9676
-0.8053
2.5934
0.7375
1.7206
-0.0863
0.6051
-0.1528
-0.4384
-0.0117
0.0289
0.3969
0.5164
0.098
0.2103
0.1043
0.0177
0.0165
-0.0538
0.004
14.9569
-25.0164
7.472
37
10.0149
-3.4794
-2.4654
2.6254
-2.1579
10.1691
0.6153
-0.2172
0.6397
-0.0889
-0.1719
-0.6496
-0.0482
1.2894
-0.4434
-0.0406
0.1132
0.0443
-0.0208
-0.0495
0.1156
23.7998
-26.4662
14.5903
38
3.4671
-2.3297
0.1618
2.1136
0.5646
5.6134
0.5114
0.2643
-0.2438
-0.1112
-0.3332
0.5148
1.3767
0.1247
-0.1781
0.1442
-0.0139
-0.1079
-0.1325
-0.0151
0.1614
9.2518
-32.4333
10.6364
39
7.3753
-0.6383
-1.239
2.6374
-0.401
5.2642
-0.1434
0.1094
-0.1564
0.1503
-0.0019
0.1323
0.7825
0.1143
0.1453
0.1613
-0.0427
0.0063
-0.0411
-0.0061
-0.0451
9.688
-29.6487
21.719
40
6.9898
-2.0838
1.4342
4.048
0.342
0.4671
-0.0622
0.3813
-0.4695
-0.2996
0.1523
0.3668
0.0922
-0.1348
-0.0901
0.0297
-0.0977
-0.0396
0.0718
0.034
0.0025
7.3654
-22.065
15.8635
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
424 - 441
2
X-RAY DIFFRACTION
2
A
442 - 463
3
X-RAY DIFFRACTION
3
A
464 - 477
4
X-RAY DIFFRACTION
4
A
478 - 492
5
X-RAY DIFFRACTION
5
A
493 - 516
6
X-RAY DIFFRACTION
6
A
517 - 524
7
X-RAY DIFFRACTION
7
A
525 - 553
8
X-RAY DIFFRACTION
8
A
554 - 581
9
X-RAY DIFFRACTION
9
A
582 - 597
10
X-RAY DIFFRACTION
10
A
598 - 603
11
X-RAY DIFFRACTION
11
B
426 - 442
12
X-RAY DIFFRACTION
12
B
443 - 460
13
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13
B
461 - 475
14
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14
B
476 - 488
15
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15
B
489 - 499
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16
B
500 - 507
17
X-RAY DIFFRACTION
17
B
508 - 532
18
X-RAY DIFFRACTION
18
B
533 - 568
19
X-RAY DIFFRACTION
19
B
569 - 584
20
X-RAY DIFFRACTION
20
B
585 - 605
21
X-RAY DIFFRACTION
21
C
424 - 441
22
X-RAY DIFFRACTION
22
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442 - 464
23
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465 - 480
24
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C
481 - 490
25
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C
491 - 505
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C
506 - 519
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27
C
520 - 544
28
X-RAY DIFFRACTION
28
C
545 - 567
29
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29
C
568 - 591
30
X-RAY DIFFRACTION
30
C
592 - 602
31
X-RAY DIFFRACTION
31
D
425 - 435
32
X-RAY DIFFRACTION
32
D
436 - 454
33
X-RAY DIFFRACTION
33
D
455 - 479
34
X-RAY DIFFRACTION
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D
480 - 498
35
X-RAY DIFFRACTION
35
D
499 - 507
36
X-RAY DIFFRACTION
36
D
508 - 520
37
X-RAY DIFFRACTION
37
D
526 - 542
38
X-RAY DIFFRACTION
38
D
543 - 563
39
X-RAY DIFFRACTION
39
D
564 - 583
40
X-RAY DIFFRACTION
40
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584 - 604
+
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