Mass: 39827.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0884 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KL63
Method to determine structure: MOLECULAR REPLACEMENT Starting model: the same protein structure from SAD phasing with a lower resolution. Resolution: 1.75→49.49 Å / SU ML: 0.2106 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.6169
Rfactor
Num. reflection
% reflection
Rfree
0.1965
3656
4.94 %
Rwork
0.1745
-
-
obs
0.1756
74012
97.32 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parameters
Biso mean: 40.53 Å2
Refinement step
Cycle: LAST / Resolution: 1.75→49.49 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5556
0
13
323
5892
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.0032
5743
X-RAY DIFFRACTION
f_angle_d
0.5328
7820
X-RAY DIFFRACTION
f_chiral_restr
0.0379
937
X-RAY DIFFRACTION
f_plane_restr
0.0026
1032
X-RAY DIFFRACTION
f_dihedral_angle_d
14.3765
3501
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.75-1.77
0.3545
112
0.3147
2424
X-RAY DIFFRACTION
87.21
1.77-1.8
0.2679
106
0.2956
2663
X-RAY DIFFRACTION
94.09
1.8-1.82
0.3096
127
0.274
2593
X-RAY DIFFRACTION
95.2
1.82-1.85
0.2771
129
0.2566
2679
X-RAY DIFFRACTION
96.73
1.85-1.88
0.2934
142
0.2269
2697
X-RAY DIFFRACTION
97.76
1.88-1.91
0.2213
146
0.2142
2698
X-RAY DIFFRACTION
97.77
1.91-1.94
0.242
143
0.2012
2679
X-RAY DIFFRACTION
97.78
1.94-1.98
0.2512
150
0.2048
2699
X-RAY DIFFRACTION
97.87
1.98-2.02
0.2274
134
0.1916
2698
X-RAY DIFFRACTION
98.03
2.02-2.06
0.2401
140
0.1914
2646
X-RAY DIFFRACTION
95.02
2.06-2.1
0.2304
132
0.1863
2649
X-RAY DIFFRACTION
97.41
2.1-2.15
0.2079
172
0.1736
2733
X-RAY DIFFRACTION
98.24
2.15-2.21
0.2116
150
0.1579
2701
X-RAY DIFFRACTION
98.21
2.21-2.27
0.1699
146
0.1588
2725
X-RAY DIFFRACTION
98.32
2.27-2.33
0.2241
148
0.1629
2686
X-RAY DIFFRACTION
98.27
2.33-2.41
0.1936
111
0.1681
2776
X-RAY DIFFRACTION
98.63
2.41-2.49
0.2422
135
0.1725
2769
X-RAY DIFFRACTION
98.64
2.49-2.59
0.2399
138
0.1775
2706
X-RAY DIFFRACTION
98.41
2.59-2.71
0.1906
129
0.1766
2677
X-RAY DIFFRACTION
96
2.71-2.85
0.2129
162
0.1727
2751
X-RAY DIFFRACTION
98.91
2.85-3.03
0.2046
147
0.1824
2753
X-RAY DIFFRACTION
99.38
3.03-3.27
0.2144
137
0.1788
2817
X-RAY DIFFRACTION
99.49
3.27-3.6
0.1832
139
0.1721
2780
X-RAY DIFFRACTION
99.25
3.6-4.12
0.1836
176
0.1498
2696
X-RAY DIFFRACTION
96.77
4.12-5.18
0.1422
175
0.1464
2776
X-RAY DIFFRACTION
99.43
5.18-49.49
0.1801
130
0.1797
2885
X-RAY DIFFRACTION
97.54
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
3.76495633048
2.51055249368
2.55048306119
3.4596848913
2.42853460052
3.43505862973
-0.0490115376066
0.166057077371
0.0776616541729
-0.123618523336
-0.0494558159488
0.00840506082771
-0.0229041651197
-0.102311580967
-0.0586340705324
0.222570588482
0.0578156999097
0.00375051906128
0.289394646859
0.0280513278291
0.179977589296
8.60776466807
4.86560944899
21.9706272005
2
5.52365078793
1.48773966527
2.12256587925
1.69859073767
0.894009365251
3.09890289281
0.219106783491
0.063100142039
0.59130685203
0.208097009678
-0.280996916215
0.133427021149
0.101118527475
-0.119143587188
0.137552152922
0.240570298354
0.0594209705959
0.00838101945011
0.238114916259
0.0274719299606
0.261996030891
9.34670035187
18.068884238
30.3073291874
3
3.38969539047
1.36440902671
1.63344108686
1.70699306597
1.1905578455
1.64220411508
-0.150914365799
0.249443125732
0.00630753095358
-0.296793336026
-0.0787372155473
0.229373953449
0.015219104934
-0.331306407376
0.260377110878
0.30728144515
-0.00192029611141
0.00298536741326
0.52541754406
0.000673785192674
0.261562492733
-7.51641811996
2.03711952218
12.7640564367
4
8.68635248904
5.88727269359
1.91540182534
6.83005129739
1.15240255547
2.50048259213
-0.415569624566
1.1923508387
0.384820872042
-0.493110119661
0.459666119617
0.204709969311
-0.117583088251
0.225169315935
-0.0317132021621
0.233277020242
0.0352805284914
0.0137949218396
0.439374887555
0.0607189769572
0.202774811431
27.4647502546
9.84146200774
21.3461935099
5
0.942332760832
-0.615857786995
-0.739328882197
0.818920724251
-0.354750973204
2.21783240232
-0.0349162363262
0.71968958439
-0.764926960595
-0.244921633177
0.2569420299
-0.379380242486
0.392434486424
-0.10709792377
0.107991927695
0.308968257072
0.00154708756934
-0.0110251078068
0.336955932489
-0.100869077178
0.312544969473
13.3877146094
-3.29740594716
26.5368980843
6
4.36314921584
3.19311233042
2.85347171735
2.91926601588
2.93641751239
3.02950922044
0.149741465399
-0.101688475276
-0.0491430258124
0.193264516621
-0.11648631339
-0.0612795357426
0.205462983521
-0.195471405011
-0.0851298592211
0.260707268198
-0.0171339638857
-0.0111652397172
0.290244405756
0.0276992364013
0.248098915543
20.9673723267
5.72052636264
33.4221602513
7
4.45899138407
2.56962510644
2.06142903224
3.38981771432
1.74236194607
1.97865695224
0.100326125198
0.435713136045
-0.252899798205
0.0796705028956
0.134355850673
-0.403439997106
0.14437477406
0.240696992973
-0.23618158645
0.195033437462
0.0459180919125
0.00851837558714
0.266703836657
0.00529054884791
0.225552811444
30.7123696817
7.36903485692
29.9153046422
8
7.82512528887
4.43860973261
5.19719199538
3.72619747295
3.52619908804
4.52897904749
-0.420717836106
0.706833973394
0.0335307014626
-0.515536797766
0.199854772592
0.197777292509
-0.289740936363
0.0419767299685
0.244701218779
0.367115498767
0.0107843829128
-0.00371818519103
0.553986637262
-0.00459357513023
0.26693255159
0.47633583285
4.34895820078
9.83445631471
9
6.02239259164
2.22531071823
4.78491483922
3.33493150338
1.79124765104
5.76907160042
0.128018478831
0.369907696241
-0.766308332755
-0.172246084558
-0.19936191264
-0.0843080219867
0.916818568598
-0.172052311518
0.0490926831014
0.484887349679
-0.10046174536
0.0428973175938
0.605385904096
-0.133163493527
0.43289205673
-11.5598267315
-13.5864446648
6.4750999977
10
0.998746862046
0.228014136167
2.28687279987
1.81214111596
0.468176617853
5.6718986674
0.754722038222
-0.3319511669
-1.10181926426
0.53263910668
-0.208868878981
-0.717484349398
0.196464862937
0.210433733897
-0.321673721275
0.35004385562
0.0293200634019
-0.078997196554
0.259122006469
0.00758725890981
0.403209496094
20.2506766241
-0.895217914989
35.4668696079
11
2.5934139896
-2.57473676851
1.40811051414
4.56351810215
-1.94470075891
1.45599047007
0.0241277953123
0.0527005550853
0.0348878704448
-0.0632173505173
-0.073126587344
-0.130277156296
0.100606366642
0.109752130256
0.0376882481595
0.22606032088
0.00321317858601
0.0234930121738
0.209529265
-0.0193866590392
0.156545556455
18.0845050185
-0.415905270794
51.5735838
12
5.94466793894
-5.18424001301
2.4308504364
5.99438478373
-2.12545360852
1.20598713578
-0.402646841778
-0.239645402753
0.324048402591
0.549763603904
0.193755506273
-0.464612351078
-0.165961843321
0.0156674452685
0.238419772358
0.251227176797
0.00319768049497
0.00981595224002
0.213112268065
0.00134955215854
0.180193501412
20.2131292349
4.25538852468
59.2776563581
13
2.97279398688
-0.691015382961
-1.04796969025
1.14793353383
0.617888109855
2.03781934134
-0.131444080202
-0.16406327545
-0.164649371043
0.181832609698
0.0601667683725
0.0573168834782
0.254075731537
-0.00395802854014
0.0508484854976
0.258646075578
-0.0357041535695
-0.00304543683218
0.189352855028
0.00892283151912
0.225943952529
-3.02547337307
1.85662074577
49.2022981386
14
2.79340542475
-1.73434227501
1.31559382022
1.98455313512
-0.81831940865
0.89932887494
-0.0612687559396
-0.207043598772
-0.0539570481205
0.0866169934465
0.0637357473481
0.0496833713383
0.0820326688575
-0.101331806066
-0.0156825414687
0.196052537106
-0.0120428550026
0.0438532638571
0.173349723738
0.0233927200333
0.147962810738
3.53581329802
2.20683594451
50.804911883
15
3.61243887152
-2.18624932221
2.5705550538
3.18831540331
-1.55300683032
3.42527256519
0.352123104399
-0.0367447101719
-0.506771683306
-0.146996295902
-0.0114018381087
0.26693709196
0.507273338044
0.129541644984
-0.299949407384
0.234614261283
-0.00422634046617
0.0254647155498
0.161028176881
-0.0074061658305
0.241025357804
19.1627870713
-14.184173174
53.6954305431
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid2through41 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid42through70 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid71through159 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid160through190 )
5
X-RAY DIFFRACTION
5
chain 'A' and (resid191through208 )
6
X-RAY DIFFRACTION
6
chain 'A' and (resid209through230 )
7
X-RAY DIFFRACTION
7
chain 'A' and (resid231through264 )
8
X-RAY DIFFRACTION
8
chain 'A' and (resid265through309 )
9
X-RAY DIFFRACTION
9
chain 'A' and (resid310through341 )
10
X-RAY DIFFRACTION
10
chain 'A' and (resid342through358 )
11
X-RAY DIFFRACTION
11
chain 'B' and (resid2through103 )
12
X-RAY DIFFRACTION
12
chain 'B' and (resid104through159 )
13
X-RAY DIFFRACTION
13
chain 'B' and (resid160through208 )
14
X-RAY DIFFRACTION
14
chain 'B' and (resid209through309 )
15
X-RAY DIFFRACTION
15
chain 'B' and (resid310through357 )
+
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