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- PDB-5ec5: Crystal structure of lysenin pore -

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Basic information

Entry
Database: PDB / ID: 5ec5
TitleCrystal structure of lysenin pore
ComponentsLysenin
KeywordsTOXIN / invertebrate cytolysin / nonamer / functional pore / nanopore
Function / homology
Function and homology information


other organism cell membrane / monoatomic ion transport / toxin activity / killing of cells of another organism / defense response to bacterium / extracellular region / membrane
Similarity search - Function
Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
: / MERCURIBENZOIC ACID / Lysenin
Similarity search - Component
Biological speciesEisenia fetida (common brandling worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsPodobnik, M. / Savory, P. / Rojko, N. / Kisovec, M. / Bruce, M. / Jayasinghe, L. / Anderluh, G.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
BioStruct-XFP7/2007-2013 Slovenia
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly.
Authors: Podobnik, M. / Savory, P. / Rojko, N. / Kisovec, M. / Wood, N. / Hambley, R. / Pugh, J. / Wallace, E.J. / McNeill, L. / Bruce, M. / Liko, I. / Allison, T.M. / Mehmood, S. / Yilmaz, N. / ...Authors: Podobnik, M. / Savory, P. / Rojko, N. / Kisovec, M. / Wood, N. / Hambley, R. / Pugh, J. / Wallace, E.J. / McNeill, L. / Bruce, M. / Liko, I. / Allison, T.M. / Mehmood, S. / Yilmaz, N. / Kobayashi, T. / Gilbert, R.J. / Robinson, C.V. / Jayasinghe, L. / Anderluh, G.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysenin
B: Lysenin
C: Lysenin
D: Lysenin
E: Lysenin
F: Lysenin
G: Lysenin
H: Lysenin
I: Lysenin
J: Lysenin
K: Lysenin
L: Lysenin
M: Lysenin
N: Lysenin
O: Lysenin
P: Lysenin
R: Lysenin
S: Lysenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)611,72854
Polymers601,84218
Non-polymers9,88636
Water1,09961
1
A: Lysenin
B: Lysenin
C: Lysenin
D: Lysenin
E: Lysenin
F: Lysenin
G: Lysenin
H: Lysenin
I: Lysenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,98527
Polymers300,9219
Non-polymers5,06418
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: Lysenin
K: Lysenin
L: Lysenin
M: Lysenin
N: Lysenin
O: Lysenin
P: Lysenin
R: Lysenin
S: Lysenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,74327
Polymers300,9219
Non-polymers4,82218
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)192.994, 192.994, 493.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112A
212M
113A
213N
114A
214O
115A
215P
116A
216R
117A
217S
118B
218C
119B
219D
120B
220E
121B
221F
122B
222G
123B
223H
124B
224I
125B
225J
126B
226K
127B
227L
128B
228M
129B
229N
130B
230O
131B
231P
132B
232R
133B
233S
134C
234D
135C
235E
136C
236F
137C
237G
138C
238H
139C
239I
140C
240J
141C
241K
142C
242L
143C
243M
144C
244N
145C
245O
146C
246P
147C
247R
148C
248S
149D
249E
150D
250F
151D
251G
152D
252H
153D
253I
154D
254J
155D
255K
156D
256L
157D
257M
158D
258N
159D
259O
160D
260P
161D
261R
162D
262S
163E
263F
164E
264G
165E
265H
166E
266I
167E
267J
168E
268K
169E
269L
170E
270M
171E
271N
172E
272O
173E
273P
174E
274R
175E
275S
176F
276G
177F
277H
178F
278I
179F
279J
180F
280K
181F
281L
182F
282M
183F
283N
184F
284O
185F
285P
186F
286R
187F
287S
188G
288H
189G
289I
190G
290J
191G
291K
192G
292L
193G
293M
194G
294N
195G
295O
196G
296P
197G
297R
198G
298S
199H
299I
1100H
2100J
1101H
2101K
1102H
2102L
1103H
2103M
1104H
2104N
1105H
2105O
1106H
2106P
1107H
2107R
1108H
2108S
1109I
2109J
1110I
2110K
1111I
2111L
1112I
2112M
1113I
2113N
1114I
2114O
1115I
2115P
1116I
2116R
1117I
2117S
1118J
2118K
1119J
2119L
1120J
2120M
1121J
2121N
1122J
2122O
1123J
2123P
1124J
2124R
1125J
2125S
1126K
2126L
1127K
2127M
1128K
2128N
1129K
2129O
1130K
2130P
1131K
2131R
1132K
2132S
1133L
2133M
1134L
2134N
1135L
2135O
1136L
2136P
1137L
2137R
1138L
2138S
1139M
2139N
1140M
2140O
1141M
2141P
1142M
2142R
1143M
2143S
1144N
2144O
1145N
2145P
1146N
2146R
1147N
2147S
1148O
2148P
1149O
2149R
1150O
2150S
1151P
2151R
1152P
2152S
1153R
2153S

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A9 - 297
2111B9 - 297
1121A8 - 297
2121C8 - 297
1131A8 - 297
2131D8 - 297
1141A9 - 297
2141E9 - 297
1151A8 - 297
2151F8 - 297
1161A8 - 297
2161G8 - 297
1171A9 - 297
2171H9 - 297
1181A9 - 297
2181I9 - 297
1191A8 - 297
2191J8 - 297
11101A8 - 297
21101K8 - 297
11111A9 - 297
21111L9 - 297
11121A9 - 296
21121M9 - 296
11131A9 - 296
21131N9 - 296
11141A9 - 296
21141O9 - 296
11151A9 - 296
21151P9 - 296
11161A8 - 297
21161R8 - 297
11171A9 - 297
21171S9 - 297
11181B9 - 297
21181C9 - 297
11191B9 - 296
21191D9 - 296
11201B9 - 297
21201E9 - 297
11211B9 - 297
21211F9 - 297
11221B9 - 297
21221G9 - 297
11231B9 - 297
21231H9 - 297
11241B9 - 297
21241I9 - 297
11251B9 - 297
21251J9 - 297
11261B9 - 297
21261K9 - 297
11271B9 - 297
21271L9 - 297
11281B9 - 297
21281M9 - 297
11291B9 - 297
21291N9 - 297
11301B9 - 297
21301O9 - 297
11311B9 - 297
21311P9 - 297
11321B9 - 297
21321R9 - 297
11331B9 - 297
21331S9 - 297
11341C8 - 297
21341D8 - 297
11351C9 - 297
21351E9 - 297
11361C8 - 297
21361F8 - 297
11371C8 - 297
21371G8 - 297
11381C9 - 297
21381H9 - 297
11391C9 - 297
21391I9 - 297
11401C8 - 297
21401J8 - 297
11411C8 - 297
21411K8 - 297
11421C9 - 297
21421L9 - 297
11431C9 - 297
21431M9 - 297
11441C9 - 297
21441N9 - 297
11451C9 - 297
21451O9 - 297
11461C9 - 297
21461P9 - 297
11471C8 - 297
21471R8 - 297
11481C9 - 297
21481S9 - 297
11491D9 - 296
21491E9 - 296
11501D8 - 297
21501F8 - 297
11511D8 - 297
21511G8 - 297
11521D9 - 296
21521H9 - 296
11531D9 - 296
21531I9 - 296
11541D8 - 297
21541J8 - 297
11551D8 - 297
21551K8 - 297
11561D9 - 296
21561L9 - 296
11571D9 - 297
21571M9 - 297
11581D9 - 297
21581N9 - 297
11591D9 - 297
21591O9 - 297
11601D9 - 297
21601P9 - 297
11611D8 - 297
21611R8 - 297
11621D9 - 296
21621S9 - 296
11631E9 - 297
21631F9 - 297
11641E9 - 297
21641G9 - 297
11651E9 - 297
21651H9 - 297
11661E9 - 297
21661I9 - 297
11671E9 - 297
21671J9 - 297
11681E9 - 297
21681K9 - 297
11691E9 - 297
21691L9 - 297
11701E9 - 297
21701M9 - 297
11711E9 - 297
21711N9 - 297
11721E9 - 297
21721O9 - 297
11731E9 - 297
21731P9 - 297
11741E9 - 297
21741R9 - 297
11751E9 - 297
21751S9 - 297
11761F8 - 297
21761G8 - 297
11771F9 - 297
21771H9 - 297
11781F9 - 296
21781I9 - 296
11791F8 - 297
21791J8 - 297
11801F8 - 297
21801K8 - 297
11811F9 - 297
21811L9 - 297
11821F9 - 297
21821M9 - 297
11831F9 - 297
21831N9 - 297
11841F9 - 297
21841O9 - 297
11851F9 - 297
21851P9 - 297
11861F8 - 297
21861R8 - 297
11871F9 - 297
21871S9 - 297
11881G9 - 297
21881H9 - 297
11891G9 - 297
21891I9 - 297
11901G8 - 297
21901J8 - 297
11911G8 - 297
21911K8 - 297
11921G9 - 297
21921L9 - 297
11931G9 - 296
21931M9 - 296
11941G9 - 296
21941N9 - 296
11951G9 - 296
21951O9 - 296
11961G9 - 296
21961P9 - 296
11971G8 - 297
21971R8 - 297
11981G9 - 297
21981S9 - 297
11991H9 - 297
21991I9 - 297
111001H9 - 297
211001J9 - 297
111011H9 - 297
211011K9 - 297
111021H9 - 297
211021L9 - 297
111031H9 - 297
211031M9 - 297
111041H9 - 297
211041N9 - 297
111051H9 - 297
211051O9 - 297
111061H9 - 297
211061P9 - 297
111071H9 - 297
211071R9 - 297
111081H9 - 297
211081S9 - 297
111091I9 - 297
211091J9 - 297
111101I9 - 297
211101K9 - 297
111111I9 - 297
211111L9 - 297
111121I9 - 297
211121M9 - 297
111131I9 - 297
211131N9 - 297
111141I9 - 297
211141O9 - 297
111151I9 - 297
211151P9 - 297
111161I9 - 296
211161R9 - 296
111171I9 - 297
211171S9 - 297
111181J8 - 297
211181K8 - 297
111191J9 - 297
211191L9 - 297
111201J9 - 296
211201M9 - 296
111211J9 - 296
211211N9 - 296
111221J9 - 296
211221O9 - 296
111231J9 - 296
211231P9 - 296
111241J8 - 297
211241R8 - 297
111251J9 - 297
211251S9 - 297
111261K9 - 297
211261L9 - 297
111271K9 - 296
211271M9 - 296
111281K9 - 296
211281N9 - 296
111291K9 - 296
211291O9 - 296
111301K9 - 296
211301P9 - 296
111311K8 - 297
211311R8 - 297
111321K9 - 297
211321S9 - 297
111331L9 - 297
211331M9 - 297
111341L9 - 297
211341N9 - 297
111351L9 - 297
211351O9 - 297
111361L9 - 297
211361P9 - 297
111371L9 - 297
211371R9 - 297
111381L9 - 297
211381S9 - 297
111391M9 - 297
211391N9 - 297
111401M9 - 297
211401O9 - 297
111411M9 - 297
211411P9 - 297
111421M9 - 297
211421R9 - 297
111431M9 - 297
211431S9 - 297
111441N9 - 297
211441O9 - 297
111451N9 - 297
211451P9 - 297
111461N9 - 297
211461R9 - 297
111471N9 - 297
211471S9 - 297
111481O9 - 297
211481P9 - 297
111491O9 - 297
211491R9 - 297
111501O9 - 297
211501S9 - 297
111511P9 - 297
211511R9 - 297
111521P9 - 297
211521S9 - 297
111531R9 - 297
211531S9 - 297

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.765199, 0.643715, -0.010057), (-0.643733, 0.765248, 0.001778), (0.00884, 0.005114, 0.999948)0.17725, 100.76318, -1.45822
3given(1), (1), (1)
4given(0.175296, 0.984395, -0.015413), (-0.984478, 0.175405, 0.006038), (0.008648, 0.014116, 0.999863)64.2013, 178.26367, -1.88009
5given(1), (1), (1)
6given(-0.497049, 0.867496, -0.01983), (-0.867722, -0.496948, 0.010078), (-0.001112, 0.022216, 0.999753)163.99892, 197.29517, -0.80962
7given(1), (1), (1)
8given(-0.939685, 0.341448, -0.020155), (-0.341939, -0.939214, 0.03089), (-0.008382, 0.035919, 0.99932)253.32277, 143.81924, -0.52498
9given(1), (1), (1)
10given(-0.93727, -0.348559, -0.005614), (0.347828, -0.936136, 0.051617), (-0.023247, 0.046426, 0.998651)286.80038, 43.9383, 0.9142
11given(1), (1), (1)
12given(-0.497031, -0.867579, 0.016304), (0.86744, -0.496288, 0.035318), (-0.02255, 0.031697, 0.999243)248.67589, -47.3811, 1.53658
13given(1), (1), (1)
14given(0.177427, -0.983898, 0.021553), (0.984095, 0.177571, 0.004978), (-0.008725, 0.020327, 0.999755)160.81413, -92.34695, 0.22323
15given(1), (1), (1)
16given(0.768323, -0.640001, 0.008857), (0.640043, 0.768334, -0.002764), (-0.005037, 0.007792, 0.999957)64.14939, -74.91327, 0.28377
17given(1), (1), (1)
18given(-0.807958, 0.58916, -0.009698), (0.589227, 0.807718, -0.02008), (-0.003997, -0.021938, -0.999751)219.33975, -65.76485, 494.47531
19given(1), (1), (1)
20given(-0.997653, -0.068257, -0.005507), (-0.068099, 0.997364, -0.025055), (0.007202, -0.024621, -0.999671)279.77127, 15.60704, 493.07111
21given(1), (1), (1)
22given(-0.722058, -0.691803, 0.006361), (-0.691562, 0.721488, -0.034589), (0.01934, -0.029374, -0.999381)272.63776, 118.72429, 491.55161
23given(1), (1), (1)
24given(-0.110403, -0.993695, 0.019544), (-0.993571, 0.10985, -0.027376), (0.025056, -0.02244, -0.999434)201.50876, 191.46996, 490.40469
25given(1), (1), (1)
26given(0.555635, -0.831161, 0.021005), (-0.831218, -0.555885, -0.008359), (0.018624, -0.012815, -0.999744)100.70286, 200.20744, 490.87912
27given(1), (1), (1)
28given(0.960527, -0.27804, 0.009038), (-0.278062, -0.960562, 0.00122), (0.008342, -0.003685, -0.999958)18.15354, 143.48851, 491.82672
29given(1), (1), (1)
30given(0.914769, 0.403974, -0.001431), (0.403972, -0.91477, -0.001277), (-0.001824, 0.00059, -0.999998)-9.61145, 47.80233, 492.94073
31given(1), (1), (1)
32given(0.440935, 0.897504, -0.007982), (0.897475, -0.440992, -0.00806), (-0.010754, -0.00361, -0.999936)30.60718, -43.88541, 494.35315
33given(1), (1), (1)
34given(-0.240853, 0.97046, -0.014012), (0.970493, 0.24064, -0.01532), (-0.011496, -0.017289, -0.999784)121.95084, -88.8158, 495.26227
35given(1), (1), (1)
36given(0.767941, 0.640484, -0.006836), (-0.6405, 0.767958, -0.000226), (0.005105, 0.004552, 0.999977)-0.90234, 100.52966, -0.92487
37given(1), (1), (1)
38given(0.178585, 0.983831, -0.013551), (-0.983918, 0.178616, 0.001082), (0.003485, 0.01314, 0.999908)63.32853, 179.06519, -1.04861
39given(1), (1), (1)
40given(-0.498661, 0.866371, -0.027171), (-0.866797, -0.498379, 0.016794), (0.001008, 0.031927, 0.99949)166.08849, 195.67998, -1.70022
41given(1), (1), (1)
42given(-0.941245, 0.336492, -0.028834), (-0.337467, -0.940429, 0.041345), (-0.013205, 0.048646, 0.998729)255.93474, 140.96953, -0.63581
43given(1), (1), (1)
44given(-0.938973, -0.343987, -0.001401), (0.343615, -0.938133, 0.042845), (-0.016053, 0.039748, 0.999081)285.53531, 46.58043, 0.22738
45given(1), (1), (1)
46given(-0.498137, -0.866834, 0.021424), (0.867041, -0.497666, 0.023842), (-0.010005, 0.030452, 0.999486)247.42934, -44.55957, -0.13699
47given(1), (1), (1)
48given(0.175663, -0.984299, 0.017266), (0.984378, 0.175836, 0.009055), (-0.011949, 0.015406, 0.99981)162.11072, -93.32478, 0.83193
49given(1), (1), (1)
50given(-0.997599, -0.06919, -0.003141), (-0.069082, 0.997253, -0.026711), (0.004981, -0.02643, -0.999638)279.22736, 16.16279, 493.42648
51given(1), (1), (1)
52given(-0.719577, -0.694406, 0.003009), (-0.694203, 0.719248, -0.027654), (0.017039, -0.021988, -0.999613)273.15906, 117.28276, 491.54614
53given(1), (1), (1)
54given(-0.105872, -0.994195, 0.019189), (-0.993991, 0.105271, -0.029988), (0.027794, -0.022249, -0.999366)200.85046, 192.38622, 489.91415
55given(1), (1), (1)
56given(0.555417, -0.831236, 0.023619), (-0.831216, -0.555787, -0.013488), (0.024339, -0.01214, -0.99963)100.03499, 201.52554, 489.98019
57given(1), (1), (1)
58given(0.960433, -0.278226, 0.012564), (-0.278272, -0.9605, 0.002013), (0.011507, -0.005429, -0.999919)17.26841, 143.31944, 491.48508
59given(1), (1), (1)
60given(0.914026, 0.405643, -0.003063), (0.40565, -0.914027, 0.001761), (-0.002085, -0.002852, -0.999994)-9.29185, 46.73959, 493.21594
61given(1), (1), (1)
62given(0.439767, 0.898065, -0.009221), (0.898051, -0.439833, -0.007141), (-0.010469, -0.005141, -0.999932)31.0178, -44.28672, 494.40356
63given(1), (1), (1)
64given(-0.240594, 0.970578, -0.009594), (0.970525, 0.240414, -0.01682), (-0.014019, -0.013358, -0.999812)120.76087, -88.46516, 495.26715
65given(1), (1), (1)
66given(-0.809364, 0.587239, -0.008989), (0.587246, 0.808962, -0.026893), (-0.008521, -0.027045, -0.999598)219.45662, -63.84072, 495.27426
67given(1), (1), (1)
68given(0.767273, 0.641301, -0.004935), (-0.641318, 0.767268, -0.003371), (0.001625, 0.005751, 0.999982)-1.20251, 101.49214, -0.39604
69given(1), (1), (1)
70given(0.172078, 0.984753, -0.025498), (-0.985074, 0.172133, -4.5E-5), (0.004345, 0.025126, 0.999675)67.08739, 180.06239, -1.82166
71given(1), (1), (1)
72given(-0.50671, 0.861025, -0.043375), (-0.862092, -0.506436, 0.017916), (-0.00654, 0.046471, 0.998898)171.29698, 195.53809, -1.48918
73given(1), (1), (1)
74given(-0.941239, 0.336936, -0.023321), (-0.337605, -0.940578, 0.036562), (-0.009616, 0.042287, 0.999059)254.50531, 142.03291, -0.80366
75given(1), (1), (1)
76given(-0.937878, -0.346888, 0.007319), (0.346917, -0.937186, 0.036481), (-0.005796, 0.036754, 0.999308)283.41006, 47.63657, -0.99471
77given(1), (1), (1)
78given(-0.495717, -0.868391, 0.012706), (0.868381, -0.49538, 0.022665), (-0.013388, 0.022269, 0.999662)249.33273, -44.47275, 0.68475
79given(1), (1), (1)
80given(-0.721796, -0.69204, 0.009518), (-0.692003, 0.721386, -0.027095), (0.011885, -0.026144, -0.999588)271.70352, 116.88846, 492.43524
81given(1), (1), (1)
82given(-0.107826, -0.994059, 0.014836), (-0.993923, 0.107455, -0.023867), (0.022131, -0.017319, -0.999605)202.26576, 190.64305, 490.57767
83given(1), (1), (1)
84given(0.555303, -0.831181, 0.027873), (-0.831174, -0.555806, -0.015136), (0.028073, -0.014762, -0.999497)98.9037, 201.97157, 489.51913
85given(1), (1), (1)
86given(0.959052, -0.282405, 0.021623), (-0.282475, -0.959275, 0.000205), (0.020685, -0.006304, -0.999766)15.3445, 144.44534, 490.1875
87given(1), (1), (1)
88given(0.915835, 0.401543, 0.003238), (0.401525, -0.915834, 0.005017), (0.00498, -0.003295, -0.999982)-10.93398, 46.74087, 492.26791
89given(1), (1), (1)
90given(0.44208, 0.896934, -0.008613), (0.896936, -0.44213, -0.005162), (-0.008438, -0.005443, -0.99995)30.54129, -44.43354, 494.20276
91given(1), (1), (1)
92given(-0.237551, 0.971345, -0.007666), (0.971279, 0.237409, -0.015953), (-0.013676, -0.011236, -0.999843)119.81287, -88.511, 495.1358
93given(1), (1), (1)
94given(-0.806492, 0.591241, -0.001896), (0.591113, 0.806241, -0.023686), (-0.012476, -0.020223, -0.999718)217.07805, -64.93533, 495.38879
95given(1), (1), (1)
96given(-0.997733, -0.067166, 0.004186), (-0.067263, 0.997258, -0.030869), (-0.002102, -0.03108, -0.999515)277.31125, 17.12138, 494.60455
97given(1), (1), (1)
98given(0.763804, 0.6452, -0.017902), (-0.645412, 0.763761, -0.010613), (0.006825, 0.019661, 0.999783)2.00315, 104.06078, -2.02709
99given(1), (1), (1)
100given(0.164152, 0.985493, -0.043107), (-0.986435, 0.163947, -0.008264), (-0.001077, 0.043879, 0.999036)72.02298, 182.75632, -2.26438
101given(1), (1), (1)
102given(-0.505412, 0.861946, -0.040093), (-0.862869, -0.505069, 0.019026), (-0.00385, 0.044211, 0.999015)170.24141, 195.05125, -1.82459
103given(1), (1), (1)
104given(-0.942093, 0.334962, -0.016142), (-0.335343, -0.94131, 0.038473), (-0.002307, 0.041658, 0.999129)252.90816, 141.19225, -1.82627
105given(1), (1), (1)
106given(-0.937303, -0.3485, -0.003105), (0.348239, -0.93688, 0.031386), (-0.013847, 0.028336, 0.999503)285.83017, 48.66884, 0.33145
107given(1), (1), (1)
108given(-0.109819, -0.993677, 0.023367), (-0.993793, 0.109351, -0.020424), (0.01774, -0.025465, -0.999518)200.21512, 189.66919, 491.43695
109given(1), (1), (1)
110given(0.554844, -0.831567, 0.02539), (-0.831543, -0.555271, -0.014487), (0.026145, -0.013075, -0.999573)99.63286, 201.68648, 489.64758
111given(1), (1), (1)
112given(0.958987, -0.282046, 0.02817), (-0.282172, -0.959364, 0.000527), (0.026876, -0.008454, -0.999603)13.56731, 144.20728, 489.26373
113given(1), (1), (1)
114given(0.916984, 0.398639, 0.015099), (0.398554, -0.917107, 0.008362), (0.017181, -0.00165, -0.999851)-14.12007, 46.34328, 490.29926
115given(1), (1), (1)
116given(0.445117, 0.89547, -0.002113), (0.895472, -0.445118, 0.000327), (-0.000648, -0.002037, -0.999998)28.3914, -45.46955, 492.83517
117given(1), (1), (1)
118given(-0.236157, 0.971703, -0.004726), (0.971619, 0.236062, -0.015211), (-0.013665, -0.008184, -0.999873)118.71221, -88.77384, 494.91089
119given(1), (1), (1)
120given(-0.805278, 0.59289, 0.003018), (0.592682, 0.805112, -0.022846), (-0.015975, -0.016609, -0.999734)215.4529, -65.33282, 495.57236
121given(1), (1), (1)
122given(-0.997909, -0.063494, 0.012084), (-0.063782, 0.997645, -0.025206), (-0.010455, -0.025924, -0.999609)275.0303, 15.16534, 495.26114
123given(1), (1), (1)
124given(-0.722373, -0.691172, 0.02138), (-0.691496, 0.721883, -0.02678), (0.003076, -0.034129, -0.999413)268.60861, 116.73736, 493.89941
125given(1), (1), (1)
126given(0.762068, 0.647162, -0.020809), (-0.647464, 0.761959, -0.014451), (0.006504, 0.024486, 0.999679)2.69451, 105.26134, -2.33158
127given(1), (1), (1)
128given(0.170889, 0.984629, -0.036089), (-0.985186, 0.17129, 0.008307), (0.014361, 0.034135, 0.999314)69.77235, 178.04179, -3.77565
129given(1), (1), (1)
130given(-0.503183, 0.863647, -0.030341), (-0.863991, -0.502027, 0.038586), (0.018093, 0.04563, 0.998795)167.6823, 190.25145, -4.68186
131given(1), (1), (1)
132given(-0.940773, 0.338668, -0.015834), (-0.339037, -0.939853, 0.041606), (-0.000791, 0.04451, 0.999009)252.5616, 140.86549, -2.13123
133given(1), (1), (1)
134given(0.557652, -0.829721, 0.024234), (-0.829523, -0.558109, -0.020175), (0.030265, -0.008852, -0.999503)99.5015, 202.97197, 488.89868
135given(1), (1), (1)
136given(0.960659, -0.276863, 0.021941), (-0.276599, -0.960879, -0.014312), (0.025045, 0.00768, -0.999657)14.91059, 147.21255, 488.78412
137given(1), (1), (1)
138given(0.914783, 0.403691, 0.014352), (0.403746, -0.914871, -0.001056), (0.012704, 0.006761, -0.999896)-13.72483, 47.77768, 490.55106
139given(1), (1), (1)
140given(0.443278, 0.896384, -0.000662), (0.896378, -0.443277, -0.003504), (-0.003434, 0.000959, -0.999994)28.28933, -44.81433, 493.11536
141given(1), (1), (1)
142given(-0.237956, 0.971238, -0.008624), (0.971107, 0.23774, -0.020742), (-0.018095, -0.013311, -0.999748)120.03117, -87.46052, 495.86429
143given(1), (1), (1)
144given(-0.807566, 0.589776, -0.000596), (0.589446, 0.807079, -0.034297), (-0.019746, -0.028049, -0.999411)216.98613, -62.21744, 496.7858
145given(1), (1), (1)
146given(-0.997707, -0.066898, 0.010247), (-0.06722, 0.99712, -0.035129), (-0.007868, -0.035738, -0.99933)275.75281, 18.11685, 495.46982
147given(1), (1), (1)
148given(-0.721083, -0.692595, 0.018732), (-0.692802, 0.720457, -0.031099), (0.008044, -0.035403, -0.999341)269.28961, 118.04181, 493.24487
149given(1), (1), (1)
150given(-0.105438, -0.994065, 0.026791), (-0.994152, 0.104738, -0.026301), (0.023338, -0.029407, -0.999295)198.83914, 191.4431, 490.91254
151given(1), (1), (1)
152given(0.768284, 0.639563, -0.026443), (-0.639617, 0.768657, 0.007452), (0.025091, 0.011188, 0.999623)3.99414, 98.81284, -3.89765
153given(1), (1), (1)
154given(0.176123, 0.983487, -0.041655), (-0.983509, 0.177578, 0.034278), (0.041109, 0.034931, 0.998544)70.69215, 171.45911, -7.01864
155given(1), (1), (1)
156given(-0.4974, 0.866912, -0.032511), (-0.867198, -0.495842, 0.04592), (0.023688, 0.051034, 0.998416)167.3616, 188.83904, -5.51425
157given(1), (1), (1)
158given(0.962265, -0.270957, 0.025066), (-0.27038, -0.962451, -0.024162), (0.030672, 0.016473, -0.999394)13.69053, 149.1248, 487.64304
159given(1), (1), (1)
160given(0.91129, 0.411301, 0.01956), (0.411666, -0.911088, -0.021221), (0.009093, 0.027391, -0.999583)-14.67624, 51.89224, 490.08841
161given(1), (1), (1)
162given(0.435732, 0.900062, 0.005113), (0.899995, -0.435608, -0.015964), (-0.012141, 0.011557, -0.99986)27.92206, -42.37387, 493.89304
163given(1), (1), (1)
164given(-0.242641, 0.970105, -0.0047), (0.969778, 0.242425, -0.027597), (-0.025633, -0.011254, -0.999608)119.89413, -85.65226, 496.92615
165given(1), (1), (1)
166given(-0.810239, 0.5861, 0.00041), (0.585467, 0.809395, -0.045905), (-0.027236, -0.036954, -0.998946)217.43028, -58.69592, 498.38992
167given(1), (1), (1)
168given(-0.997187, -0.073374, 0.015318), (-0.074067, 0.995947, -0.051018), (-0.011513, -0.052009, -0.99858)274.97464, 23.31318, 496.9295
169given(1), (1), (1)
170given(-0.716793, -0.696869, 0.024098), (-0.697148, 0.715538, -0.04461), (0.013844, -0.048776, -0.998714)267.73465, 122.51588, 493.2244
171given(1), (1), (1)
172given(-0.100859, -0.994509, 0.027923), (-0.99435, 0.099829, -0.036088), (0.033103, -0.031405, -0.998958)198.10382, 194.4198, 489.67935
173given(1), (1), (1)
174given(0.563523, -0.82552, 0.030958), (-0.825137, -0.56428, -0.027157), (0.039887, -0.010241, -0.999152)96.87405, 204.67763, 487.75998
175given(1), (1), (1)
176given(0.765517, 0.642768, -0.028875), (-0.642758, 0.765992, 0.010845), (0.029089, 0.010258, 0.999524)4.69022, 98.45282, -4.34047
177given(1), (1), (1)
178given(0.173232, 0.984444, -0.029339), (-0.984412, 0.173992, 0.025688), (0.030394, 0.024432, 0.999239)67.88451, 173.65674, -5.26835
179given(1), (1), (1)
180given(0.912775, 0.408341, 0.009961), (0.408446, -0.912685, -0.01332), (0.003652, 0.016226, -0.999862)-12.48536, 50.19841, 491.43646
181given(1), (1), (1)
182given(0.436598, 0.89965, 0.003558), (0.899583, -0.436509, -0.014483), (-0.011477, 0.009524, -0.999889)28.09904, -42.65811, 493.89401
183given(1), (1), (1)
184given(-0.241157, 0.970426, -0.010791), (0.970335, 0.240909, -0.020338), (-0.017137, -0.015376, -0.999735)121.12874, -87.61003, 495.94345
185given(1), (1), (1)
186given(-0.807578, 0.58966, -0.010898), (0.589641, 0.806905, -0.035045), (-0.011871, -0.034727, -0.999326)219.60606, -62.1192, 496.1669
187given(1), (1), (1)
188given(-0.997615, -0.068855, 0.004883), (-0.069007, 0.996566, -0.045767), (-0.001715, -0.045995, -0.99894)277.27463, 21.02485, 495.30859
189given(1), (1), (1)
190given(-0.718761, -0.694994, 0.019145), (-0.695113, 0.717779, -0.040139), (0.014155, -0.042158, -0.999011)269.07669, 120.81926, 492.90613
191given(1), (1), (1)
192given(-0.104162, -0.994313, 0.022179), (-0.994184, 0.103484, -0.029814), (0.02735, -0.025155, -0.999309)199.8483, 192.424, 490.18585
193given(1), (1), (1)
194given(0.55937, -0.828689, 0.019476), (-0.828433, -0.559692, -0.021072), (0.028363, -0.004347, -0.999588)100.3581, 203.16066, 488.96802
195given(1), (1), (1)
196given(0.961744, -0.273475, 0.01614), (-0.2733, -0.961851, -0.012248), (0.018873, 0.007368, -0.999795)15.95645, 146.26698, 489.80109
197given(1), (1), (1)
198given(0.766298, 0.642409, -0.009863), (-0.642318, 0.766359, 0.011059), (0.014662, -0.002139, 0.99989)-0.00498, 98.20607, -1.93083
199given(1), (1), (1)
200given(0.436642, 0.899544, -0.012842), (0.899441, -0.4368, -0.014553), (-0.018701, -0.005196, -0.999812)32.24633, -42.74747, 495.54501
201given(1), (1), (1)
202given(-0.243941, 0.969645, -0.016765), (0.969677, 0.243612, -0.019483), (-0.014808, -0.021009, -0.99967)122.9845, -87.8166, 495.84601
203given(1), (1), (1)
204given(-0.808877, 0.587471, -0.024419), (0.587978, 0.808215, -0.032703), (0.000524, -0.04081, -0.999167)223.3372, -62.55288, 494.64099
206given(1), (1), (1)
207given(-0.997576, -0.06801, -0.014739), (-0.067297, 0.996742, -0.04445), (0.017714, -0.04335, -0.998903)282.24228, 20.33462, 492.35547
208given(1), (1), (1)
209given(-0.719619, -0.694356, 0.00417), (-0.693858, 0.718847, -0.042654), (0.026619, -0.033588, -0.999081)272.9744, 121.10504, 490.67255
210given(1), (1), (1)
211given(-0.103305, -0.994579, 0.01184), (-0.994269, 0.102929, -0.028899), (0.027524, -0.014757, -0.999512)202.40175, 192.20667, 489.62482
212given(1), (1), (1)
213given(0.559932, -0.828508, 0.007106), (-0.828302, -0.559956, -0.019112), (0.019814, 0.004816, -0.999792)103.40138, 202.57297, 489.62817
214given(1), (1), (1)
215given(0.961541, -0.274661, -0.000704), (-0.274644, -0.961446, -0.01385), (0.003127, 0.013511, -0.999904)20.29459, 146.74086, 491.45892
216given(1), (1), (1)
217given(0.912423, 0.409152, -0.008842), (0.409075, -0.912453, -0.009261), (-0.011857, 0.004833, -0.999918)-7.73898, 48.92838, 494.09808
218given(1), (1), (1)
219given(-0.243422, 0.969802, -0.015186), (0.969832, 0.243159, -0.017298), (-0.013084, -0.018938, -0.999735)122.5565, -88.35737, 495.54819
220given(1), (1), (1)
221given(-0.81001, 0.586223, -0.015021), (0.586413, 0.809669, -0.023576), (-0.001659, -0.027905, -0.999609)221.04266, -64.60844, 494.45001
222given(1), (1), (1)
223given(-0.997497, -0.069611, -0.012403), (-0.069086, 0.99686, -0.03869), (0.015058, -0.037737, -0.999174)281.69931, 19.24576, 492.52957
224given(1), (1), (1)
225given(-0.720912, -0.693022, 0.002587), (-0.692507, 0.720222, -0.04141), (0.026834, -0.031645, -0.999139)273.55212, 120.59566, 490.58203
226given(1), (1), (1)
227given(-0.105353, -0.994307, 0.015942), (-0.994094, 0.104883, -0.027865), (0.026034, -0.018783, -0.999485)201.69484, 191.85922, 490.11111
228given(1), (1), (1)
229given(0.559925, -0.828442, 0.012957), (-0.828358, -0.560062, -0.012395), (0.017526, -0.003792, -0.999839)101.92921, 201.01085, 490.54688
230given(1), (1), (1)
231given(0.961416, -0.27508, 0.003036), (-0.27505, -0.961397, -0.00796), (0.005108, 0.006818, -0.999964)19.40988, 145.35703, 491.64017
232given(1), (1), (1)
233given(0.913263, 0.407322, -0.006288), (0.407263, -0.913268, -0.008915), (-0.009374, 0.005581, -0.999941)-8.39067, 49.16995, 493.67032
234given(1), (1), (1)
235given(0.436217, 0.899707, -0.015528), (0.899692, -0.436394, -0.010693), (-0.016397, -0.009306, -0.999822)33.01255, -43.7837, 495.51321
236given(1), (1), (1)
237given(0.765921, 0.642904, -0.006324), (-0.642924, 0.765929, -0.001557), (0.003843, 0.005258, 0.999979)-0.87362, 101.35936, -0.81643
238given(1), (1), (1)
239given(0.175739, 0.984207, -0.021284), (-0.984436, 0.175732, -0.002186), (0.001589, 0.021337, 0.999771)65.5992, 180.46194, -1.30131
240given(1), (1), (1)
241given(-0.496314, 0.867693, -0.027951), (-0.868134, -0.496202, 0.011322), (-0.004045, 0.029884, 0.999545)165.99579, 197.35997, -0.92083
242given(1), (1), (1)
243given(-0.938768, 0.344082, -0.017925), (-0.344471, -0.938393, 0.027554), (-0.007339, 0.032041, 0.99946)252.58981, 145.01823, -0.59166
244given(1), (1), (1)
245given(-0.939957, -0.341283, -0.002609), (0.341079, -0.93961, 0.028237), (-0.012088, 0.025652, 0.999598)285.86444, 50.55634, 0.40079
246given(1), (1), (1)
247given(-0.501093, -0.865382, 0.004376), (0.865261, -0.500921, 0.020057), (-0.015165, 0.013837, 0.999789)251.91667, -43.11729, 1.47652
248given(1), (1), (1)
249given(0.172792, -0.98494, 0.00599), (0.98489, 0.172848, 0.010705), (-0.011579, 0.00405, 0.999925)165.27213, -93.52564, 1.49194
250given(1), (1), (1)
251given(0.766574, -0.642123, 0.00651), (0.642129, 0.766595, 0.001291), (-0.00582, 0.00319, 0.999978)65.02232, -76.0053, 0.62651
252given(1), (1), (1)
253given(0.767543, 0.640902, -0.01109), (-0.640995, 0.767475, -0.010366), (0.001868, 0.015065, 0.999885)0.06172, 103.38969, -1.01074
254given(1), (1), (1)
255given(0.177921, 0.983732, -0.024818), (-0.984045, 0.177877, -0.003996), (0.000484, 0.025133, 0.999684)66.08846, 180.80136, -1.31326
256given(1), (1), (1)
257given(-0.497656, 0.866936, -0.027573), (-0.867374, -0.497434, 0.014885), (-0.000812, 0.031324, 0.999509)166.06889, 196.37659, -1.45405
258given(1), (1), (1)
259given(-0.939294, 0.342726, -0.016282), (-0.343048, -0.938978, 0.025249), (-0.006635, 0.029302, 0.999549)252.2859, 145.41765, -0.52436
260given(1), (1), (1)
261given(-0.940127, -0.340777, -0.005669), (0.340563, -0.939928, 0.02348), (-0.013329, 0.020143, 0.999708)286.50507, 51.84782, 0.91418
262given(1), (1), (1)
263given(-0.50095, -0.865475, 0.001508), (0.865364, -0.500856, 0.017002), (-0.01396, 0.009822, 0.999854)252.57375, -42.34972, 1.54607
264given(1), (1), (1)
265given(0.174269, -0.984666, 0.007982), (0.984632, 0.174346, 0.010178), (-0.011414, 0.006085, 0.999916)164.51338, -93.40614, 1.27475
266given(1), (1), (1)
267given(0.767244, 0.641192, -0.014466), (-0.641297, 0.767283, -0.003824), (0.008648, 0.012212, 0.999888)1.02614, 101.71766, -1.82421
268given(1), (1), (1)
269given(0.173948, 0.984337, -0.028702), (-0.984661, 0.17426, 0.008749), (0.013614, 0.026739, 0.99955)67.78592, 177.77383, -3.22913
270given(1), (1), (1)
271given(-0.501153, 0.864943, -0.026818), (-0.865325, -0.500623, 0.024269), (0.007566, 0.035369, 0.999346)166.67287, 193.83818, -2.79137
272given(1), (1), (1)
273given(-0.939987, 0.340776, -0.017236), (-0.341156, -0.939545, 0.029458), (-0.006155, 0.03357, 0.999417)252.84406, 144.02797, -0.7511
274given(1), (1), (1)
275given(-0.939263, -0.343101, -0.00816), (0.342741, -0.938974, 0.029276), (-0.017707, 0.024701, 0.999538)287.31049, 49.98693, 1.29946
276given(1), (1), (1)
277given(-0.497535, -0.867443, 0.001188), (0.867117, -0.49731, 0.028122), (-0.023804, 0.015022, 0.999604)252.46005, -45.62392, 2.53833
278given(1), (1), (1)
279given(0.764982, 0.643769, -0.019083), (-0.643877, 0.765129, 0.000647), (0.015018, 0.011792, 0.999818)2.46709, 101.12187, -2.68663
280given(1), (1), (1)
281given(0.170452, 0.984989, -0.02726), (-0.985201, 0.170865, 0.013589), (0.018043, 0.02454, 0.999536)67.94796, 176.89594, -3.69034
282given(1), (1), (1)
283given(-0.502431, 0.864295, -0.023614), (-0.864574, -0.501945, 0.023738), (0.008664, 0.032342, 0.999439)166.11407, 193.94476, -2.73083
284given(1), (1), (1)
285given(-0.940667, 0.338947, -0.016124), (-0.339291, -0.940216, 0.029577), (-0.005135, 0.033293, 0.999432)252.80139, 143.85294, -0.85719
286given(1), (1), (1)
287given(-0.937952, -0.346665, -0.00827), (0.346199, -0.937518, 0.034717), (-0.019789, 0.0297, 0.999363)287.38513, 48.14719, 1.26239
288given(1), (1), (1)
289given(0.765015, 0.643847, -0.014596), (-0.643857, 0.765132, 0.004641), (0.014156, 0.005847, 0.999883)1.28823, 100.11702, -2.20488
290given(1), (1), (1)
291given(0.172462, 0.984845, -0.01834), (-0.984857, 0.172739, 0.014748), (0.017693, 0.015519, 0.999723)65.41969, 176.3709, -3.10731
292given(1), (1), (1)
293given(-0.501308, 0.865111, -0.016503), (-0.865177, -0.500887, 0.024104), (0.012587, 0.026362, 0.999573)164.06946, 193.8553, -2.93113
294given(1), (1), (1)
295given(-0.940758, 0.338796, -0.013833), (-0.339073, -0.940178, 0.033072), (-0.0018, 0.035803, 0.999357)252.18102, 142.91342, -1.51448
296given(1), (1), (1)
297given(0.766299, 0.642415, -0.009379), (-0.642396, 0.766354, 0.005324), (0.010608, 0.001945, 0.999942)-0.0466, 99.6276, -1.48533
298given(1), (1), (1)
299given(0.173864, 0.984675, -0.013658), (-0.984637, 0.174051, 0.014009), (0.016172, 0.011012, 0.999809)64.05852, 176.41481, -2.67138
300given(1), (1), (1)
301given(-0.501305, 0.865096, -0.017403), (-0.865203, -0.500912, 0.022602), (0.010835, 0.026388, 0.999593)164.28844, 194.18668, -2.81911
302given(1), (1), (1)
303given(0.76597, 0.642817, -0.008703), (-0.642815, 0.766014, 0.003488), (0.008908, 0.002923, 0.999956)-0.26098, 100.13169, -1.3491
304given(1), (1), (1)
305given(0.171837, 0.984977, -0.017098), (-0.985069, 0.171986, 0.007693), (0.010518, 0.015521, 0.999824)65.12219, 178.13622, -2.32244
306given(1), (1), (1)
307given(0.764944, 0.644032, -0.009155), (-0.644072, 0.764962, -0.00214), (0.005625, 0.007534, 0.999956)-0.0644, 101.76698, -1.27344

-
Components

#1: Protein
Lysenin / efL1


Mass: 33435.676 Da / Num. of mol.: 18 / Mutation: E84Q/E85K/E92Q/E97S/D126G
Source method: isolated from a genetically manipulated source
Details: protomer of the nonameric pore / Source: (gene. exp.) Eisenia fetida (common brandling worm)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O18423
#2: Chemical...
ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C7H5HgO2
#3: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.82 Å3/Da / Density % sol: 67.82 % / Description: thick plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, magnesium chloride, Hepes

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 10, 2015
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 160505 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rsym value: 0.2 / Net I/σ(I): 8.9
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSVERSION November 3, 2014data reduction
XDSVERSION November 3, 2014data scaling
PHENIX1.9-1692phasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→49.1 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.882 / SU B: 19.229 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25787 8448 5 %RANDOM
Rwork0.2144 ---
obs0.21658 160505 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.382 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å20 Å20 Å2
2--3.04 Å20 Å2
3----6.08 Å2
Refinement stepCycle: 1 / Resolution: 3.1→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40953 0 234 61 41248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01942071
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.94156969
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72555124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39523.811845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.067157308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91415234
X-RAY DIFFRACTIONr_chiral_restr0.110.26299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02131476
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7495.57620580
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.6638.35625676
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4335.83521491
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.56146.51759005
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B452TIGHT POSITIONAL0.160.21
1B442TIGHT POSITIONAL0.140.21
1B450TIGHT POSITIONAL0.140.21
1B450TIGHT POSITIONAL0.150.21
1B450TIGHT POSITIONAL0.150.21
1B450TIGHT POSITIONAL0.140.21
1B441TIGHT POSITIONAL0.130.21
1B441TIGHT POSITIONAL0.130.21
1B444TIGHT POSITIONAL0.130.21
1B440TIGHT POSITIONAL0.170.21
1B444TIGHT THERMAL5.12.06
2C441TIGHT POSITIONAL0.180.21
2C440TIGHT POSITIONAL0.170.21
2C444TIGHT POSITIONAL0.180.21
2C441TIGHT POSITIONAL0.20.21
2C440TIGHT POSITIONAL0.150.21
2C444TIGHT POSITIONAL0.150.21
2C444TIGHT POSITIONAL0.150.21
2C442TIGHT POSITIONAL0.250.21
2C444TIGHT POSITIONAL0.120.21
2C444TIGHT POSITIONAL0.130.21
2C446TIGHT THERMAL6.272.06
3D444TIGHT POSITIONAL0.130.21
3D444TIGHT POSITIONAL0.130.21
3D440TIGHT POSITIONAL0.120.21
3D441TIGHT POSITIONAL0.160.21
3D442TIGHT POSITIONAL0.130.21
3D441TIGHT POSITIONAL0.180.21
3D441TIGHT POSITIONAL0.210.21
3D446TIGHT POSITIONAL0.160.21
3D441TIGHT POSITIONAL0.150.21
3D440TIGHT POSITIONAL0.170.21
3D442TIGHT THERMAL4.222.06
4E446TIGHT POSITIONAL0.150.21
4E446TIGHT POSITIONAL0.120.21
4E442TIGHT POSITIONAL0.20.21
4E445TIGHT POSITIONAL0.130.21
4E445TIGHT POSITIONAL0.140.21
4E445TIGHT POSITIONAL0.110.21
4E445TIGHT POSITIONAL0.120.21
4E441TIGHT POSITIONAL0.120.21
4E441TIGHT POSITIONAL0.130.21
4E440TIGHT POSITIONAL0.150.21
4E441TIGHT THERMAL4.52.06
5F441TIGHT POSITIONAL0.220.21
5F442TIGHT POSITIONAL0.20.21
5F440TIGHT POSITIONAL0.140.21
5F439TIGHT POSITIONAL0.130.21
5F442TIGHT POSITIONAL0.120.21
5F442TIGHT POSITIONAL0.120.21
5F440TIGHT POSITIONAL0.150.21
5F441TIGHT POSITIONAL0.140.21
5F441TIGHT POSITIONAL0.110.21
5F441TIGHT POSITIONAL0.120.21
5F441TIGHT THERMAL5.972.06
6G441TIGHT POSITIONAL0.140.21
6G441TIGHT POSITIONAL0.150.21
6G440TIGHT POSITIONAL0.130.21
6G440TIGHT POSITIONAL0.160.21
6G441TIGHT POSITIONAL0.220.21
6G441TIGHT POSITIONAL0.20.21
6G440TIGHT POSITIONAL0.150.21
6G441TIGHT POSITIONAL0.140.21
6G441TIGHT POSITIONAL0.180.21
6G441TIGHT POSITIONAL0.180.21
6G452TIGHT THERMAL5.292.06
7H441TIGHT POSITIONAL0.140.21
7H441TIGHT POSITIONAL0.130.21
7H441TIGHT POSITIONAL0.170.21
7H441TIGHT POSITIONAL0.160.21
7H440TIGHT POSITIONAL0.150.21
7H441TIGHT POSITIONAL0.150.21
7H441TIGHT POSITIONAL0.220.21
7H440TIGHT POSITIONAL0.260.21
7H439TIGHT POSITIONAL0.210.21
7H441TIGHT POSITIONAL0.210.21
7H441TIGHT THERMAL5.542.06
8I441TIGHT POSITIONAL0.230.21
8I440TIGHT POSITIONAL0.20.21
8I440TIGHT POSITIONAL0.170.21
8I440TIGHT POSITIONAL0.190.21
8I440TIGHT POSITIONAL0.220.21
8I440TIGHT POSITIONAL0.180.21
8I441TIGHT POSITIONAL0.150.21
8I440TIGHT POSITIONAL0.180.21
8I441TIGHT POSITIONAL0.20.21
8I440TIGHT POSITIONAL0.250.21
8I440TIGHT THERMAL4.552.06
9J452TIGHT POSITIONAL0.220.21
9J452TIGHT POSITIONAL0.180.21
9J442TIGHT POSITIONAL0.160.21
9J450TIGHT POSITIONAL0.20.21
9J450TIGHT POSITIONAL0.210.21
9J450TIGHT POSITIONAL0.170.21
9J450TIGHT POSITIONAL0.180.21
9J441TIGHT POSITIONAL0.180.21
9J441TIGHT POSITIONAL0.190.21
9J440TIGHT POSITIONAL0.170.21
9J452TIGHT THERMAL4.052.06
10K441TIGHT POSITIONAL0.160.21
10K441TIGHT POSITIONAL0.130.21
10K441TIGHT POSITIONAL0.170.21
10K441TIGHT POSITIONAL0.180.21
10K441TIGHT POSITIONAL0.160.21
10K441TIGHT POSITIONAL0.150.21
10K441TIGHT POSITIONAL0.180.21
10K440TIGHT POSITIONAL0.190.21
10K441TIGHT POSITIONAL0.180.21
10K440TIGHT POSITIONAL0.130.21
10K452TIGHT THERMAL4.42.06
11L440TIGHT POSITIONAL0.160.21
11L440TIGHT POSITIONAL0.190.21
11L440TIGHT POSITIONAL0.150.21
11L440TIGHT POSITIONAL0.120.21
11L440TIGHT POSITIONAL0.160.21
11L440TIGHT POSITIONAL0.170.21
11L439TIGHT POSITIONAL0.160.21
11L440TIGHT POSITIONAL0.150.21
11L452TIGHT POSITIONAL0.150.21
11L442TIGHT POSITIONAL0.160.21
11L442TIGHT THERMAL4.62.06
12M450TIGHT POSITIONAL0.150.21
12M450TIGHT POSITIONAL0.130.21
12M450TIGHT POSITIONAL0.160.21
12M450TIGHT POSITIONAL0.150.21
12M441TIGHT POSITIONAL0.150.21
12M441TIGHT POSITIONAL0.140.21
12M442TIGHT POSITIONAL0.150.21
12M450TIGHT POSITIONAL0.160.21
12M450TIGHT POSITIONAL0.150.21
12M450TIGHT POSITIONAL0.120.21
12M450TIGHT THERMAL4.232.06
13N450TIGHT POSITIONAL0.150.21
13N441TIGHT POSITIONAL0.150.21
13N441TIGHT POSITIONAL0.150.21
13N442TIGHT POSITIONAL0.140.21
13N442TIGHT POSITIONAL0.150.21
13N442TIGHT POSITIONAL0.140.21
13N442TIGHT POSITIONAL0.130.21
13N440TIGHT POSITIONAL0.130.21
13N441TIGHT POSITIONAL0.140.21
13N451TIGHT POSITIONAL0.120.21
13N450TIGHT THERMAL6.122.06
14O451TIGHT POSITIONAL0.140.21
14O451TIGHT POSITIONAL0.120.21
14O440TIGHT POSITIONAL0.110.21
14O441TIGHT POSITIONAL0.120.21
14O451TIGHT POSITIONAL0.130.21
14O451TIGHT POSITIONAL0.130.21
14O440TIGHT POSITIONAL0.130.21
14O441TIGHT POSITIONAL0.120.21
14O451TIGHT POSITIONAL0.130.21
14O440TIGHT POSITIONAL0.130.21
14O450TIGHT THERMAL6.862.06
15P441TIGHT POSITIONAL0.130.21
15P440TIGHT POSITIONAL0.10.21
15P441TIGHT POSITIONAL0.130.21
15P440TIGHT POSITIONAL0.120.21
15P450TIGHT THERMAL7.232.06
16R441TIGHT THERMAL5.472.06
17S441TIGHT THERMAL4.942.06
18C444TIGHT THERMAL5.122.06
19D440TIGHT THERMAL4.792.06
20E441TIGHT THERMAL6.132.06
21F440TIGHT THERMAL7.392.06
22G444TIGHT THERMAL7.672.06
23H441TIGHT THERMAL7.362.06
24I440TIGHT THERMAL6.312.06
25J444TIGHT THERMAL4.872.06
26K444TIGHT THERMAL6.182.06
27L442TIGHT THERMAL6.562.06
28M444TIGHT THERMAL5.252.06
29N444TIGHT THERMAL5.272.06
30O444TIGHT THERMAL6.012.06
31P444TIGHT THERMAL5.412.06
32R440TIGHT THERMAL4.352.06
33S441TIGHT THERMAL4.462.06
34D442TIGHT THERMAL5.62.06
35E441TIGHT THERMAL7.912.06
36F441TIGHT THERMAL9.152.06
37G446TIGHT THERMAL8.82.06
38H441TIGHT THERMAL8.812.06
39I440TIGHT THERMAL7.912.06
40J446TIGHT THERMAL5.232.06
41K446TIGHT THERMAL7.512.06
42L442TIGHT THERMAL7.842.06
43M445TIGHT THERMAL5.932.06
44N445TIGHT THERMAL4.872.06
45O445TIGHT THERMAL4.572.06
46P445TIGHT THERMAL4.492.06
47R441TIGHT THERMAL4.632.06
48S441TIGHT THERMAL4.552.06
49E440TIGHT THERMAL4.882.06
50F441TIGHT THERMAL6.542.06
51G442TIGHT THERMAL6.252.06
52H440TIGHT THERMAL5.842.06
53I439TIGHT THERMAL4.912.06
54J442TIGHT THERMAL4.372.06
55K442TIGHT THERMAL4.982.06
56L440TIGHT THERMAL5.342.06
57M441TIGHT THERMAL4.292.06
58N441TIGHT THERMAL5.172.06
59O441TIGHT THERMAL5.772.06
60P441TIGHT THERMAL6.622.06
61R441TIGHT THERMAL5.172.06
62S440TIGHT THERMAL4.712.06
63F440TIGHT THERMAL4.462.06
64G441TIGHT THERMAL4.742.06
65H441TIGHT THERMAL4.32.06
66I440TIGHT THERMAL4.112.06
67J441TIGHT THERMAL5.492.06
68K441TIGHT THERMAL4.192.06
69L441TIGHT THERMAL4.322.06
70M441TIGHT THERMAL4.812.06
71N441TIGHT THERMAL6.862.06
72O441TIGHT THERMAL8.12.06
73P441TIGHT THERMAL8.532.06
74R440TIGHT THERMAL6.82.06
75S441TIGHT THERMAL6.212.06
76G441TIGHT THERMAL4.812.06
77H440TIGHT THERMAL5.162.06
78I439TIGHT THERMAL4.942.06
79J441TIGHT THERMAL6.92.06
80K441TIGHT THERMAL5.172.06
81L440TIGHT THERMAL4.892.06
82M440TIGHT THERMAL6.42.06
83N440TIGHT THERMAL7.942.06
84O440TIGHT THERMAL9.462.06
85P440TIGHT THERMAL9.542.06
86R441TIGHT THERMAL8.012.06
87S440TIGHT THERMAL7.972.06
88H441TIGHT THERMAL4.162.06
89I440TIGHT THERMAL4.912.06
90J452TIGHT THERMAL6.592.06
91K452TIGHT THERMAL4.72.06
92L442TIGHT THERMAL4.12.06
93M450TIGHT THERMAL6.042.06
94N450TIGHT THERMAL8.272.06
95O450TIGHT THERMAL9.312.06
96P450TIGHT THERMAL9.562.06
97R441TIGHT THERMAL7.922.06
98S441TIGHT THERMAL7.512.06
99I440TIGHT THERMAL4.282.06
100J441TIGHT THERMAL6.482.06
101K441TIGHT THERMAL4.392.06
102L441TIGHT THERMAL4.072.06
103M441TIGHT THERMAL5.682.06
104N441TIGHT THERMAL8.042.06
105O441TIGHT THERMAL9.12.06
106P441TIGHT THERMAL9.532.06
107R440TIGHT THERMAL7.822.06
108S441TIGHT THERMAL7.432.06
109J440TIGHT THERMAL5.212.06
110K440TIGHT THERMAL4.022.06
111L440TIGHT THERMAL4.542.06
112M440TIGHT THERMAL4.992.06
113N440TIGHT THERMAL6.852.06
114O440TIGHT THERMAL8.042.06
115P440TIGHT THERMAL8.562.06
116R439TIGHT THERMAL7.042.06
117S440TIGHT THERMAL6.342.06
118K452TIGHT THERMAL5.022.06
119L442TIGHT THERMAL5.812.06
120M450TIGHT THERMAL4.642.06
121N450TIGHT THERMAL5.012.06
122O450TIGHT THERMAL5.782.06
123P450TIGHT THERMAL6.22.06
124R441TIGHT THERMAL4.982.06
125S441TIGHT THERMAL4.312.06
126L442TIGHT THERMAL4.12.06
127M450TIGHT THERMAL5.082.06
128N450TIGHT THERMAL6.722.06
129O450TIGHT THERMAL7.572.06
130P450TIGHT THERMAL8.132.06
131R441TIGHT THERMAL6.542.06
132S441TIGHT THERMAL6.32.06
133M442TIGHT THERMAL5.232.06
134N442TIGHT THERMAL7.382.06
135O442TIGHT THERMAL8.362.06
136P442TIGHT THERMAL8.692.06
137R440TIGHT THERMAL6.722.06
138S441TIGHT THERMAL6.722.06
139N451TIGHT THERMAL5.42.06
140O451TIGHT THERMAL6.212.06
141P451TIGHT THERMAL6.72.06
142R440TIGHT THERMAL5.332.06
143S441TIGHT THERMAL4.852.06
144O451TIGHT THERMAL4.942.06
145P451TIGHT THERMAL5.232.06
146R440TIGHT THERMAL5.032.06
147S441TIGHT THERMAL4.712.06
148P451TIGHT THERMAL5.132.06
149R440TIGHT THERMAL5.792.06
150S441TIGHT THERMAL5.112.06
151R440TIGHT THERMAL5.22.06
152S441TIGHT THERMAL5.612.06
153S440TIGHT THERMAL4.432.06
LS refinement shellResolution: 3.098→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 613 -
Rwork0.341 11649 -
obs--99.56 %

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