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- PDB-9y8p: Cryo-EM structure of Thermotoga maritima encapsulin shell -

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Basic information

Entry
Database: PDB / ID: 9y8p
TitleCryo-EM structure of Thermotoga maritima encapsulin shell
ComponentsType 1 encapsulin shell protein
KeywordsVIRUS LIKE PARTICLE / ENCAPSULIN SHELL
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / iron ion transport / peptidase activity / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / :
Similarity search - Domain/homology
Type 1 encapsulin shell protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTorres, V.J. / Vera, C.S. / Cisneros, Y.W. / Portugal, R.V. / Guerra, D.G. / Evangelista, W.
Funding support Peru, 2items
OrganizationGrant numberCountry
Other governmentPROCIENCIA PE501080175-2022 Peru
Other governmentPROCIENCIA PE501089887-2024-PROCIENCIA Peru
CitationJournal: To Be Published
Title: Cryo-EM structure of Thermotoga maritima encapsulin shell
Authors: Torres, V.J. / Vera, C.S. / Cisneros, Y.W. / Portugal, R.V. / Guerra, D.G. / Evangelista, W.
History
DepositionSep 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 24, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: Type 1 encapsulin shell protein
A: Type 1 encapsulin shell protein
B: Type 1 encapsulin shell protein
C: Type 1 encapsulin shell protein
D: Type 1 encapsulin shell protein
E: Type 1 encapsulin shell protein
F: Type 1 encapsulin shell protein
G: Type 1 encapsulin shell protein
H: Type 1 encapsulin shell protein
I: Type 1 encapsulin shell protein
J: Type 1 encapsulin shell protein
K: Type 1 encapsulin shell protein
L: Type 1 encapsulin shell protein
M: Type 1 encapsulin shell protein
N: Type 1 encapsulin shell protein
O: Type 1 encapsulin shell protein
P: Type 1 encapsulin shell protein
Q: Type 1 encapsulin shell protein
R: Type 1 encapsulin shell protein
S: Type 1 encapsulin shell protein
T: Type 1 encapsulin shell protein
V: Type 1 encapsulin shell protein
W: Type 1 encapsulin shell protein
X: Type 1 encapsulin shell protein
Y: Type 1 encapsulin shell protein
Z: Type 1 encapsulin shell protein
AA: Type 1 encapsulin shell protein
BA: Type 1 encapsulin shell protein
CA: Type 1 encapsulin shell protein
DA: Type 1 encapsulin shell protein
EA: Type 1 encapsulin shell protein
FA: Type 1 encapsulin shell protein
GA: Type 1 encapsulin shell protein
HA: Type 1 encapsulin shell protein
IA: Type 1 encapsulin shell protein
JA: Type 1 encapsulin shell protein
KA: Type 1 encapsulin shell protein
LA: Type 1 encapsulin shell protein
MA: Type 1 encapsulin shell protein
NA: Type 1 encapsulin shell protein
OA: Type 1 encapsulin shell protein
PA: Type 1 encapsulin shell protein
QA: Type 1 encapsulin shell protein
RA: Type 1 encapsulin shell protein
SA: Type 1 encapsulin shell protein
TA: Type 1 encapsulin shell protein
UA: Type 1 encapsulin shell protein
VA: Type 1 encapsulin shell protein
WA: Type 1 encapsulin shell protein
XA: Type 1 encapsulin shell protein
YA: Type 1 encapsulin shell protein
ZA: Type 1 encapsulin shell protein
AB: Type 1 encapsulin shell protein
BB: Type 1 encapsulin shell protein
CB: Type 1 encapsulin shell protein
DB: Type 1 encapsulin shell protein
EB: Type 1 encapsulin shell protein
FB: Type 1 encapsulin shell protein
GB: Type 1 encapsulin shell protein
HB: Type 1 encapsulin shell protein


Theoretical massNumber of molelcules
Total (without water)1,831,00760
Polymers1,831,00760
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "TA"
d_2ens_1chain "AA"
d_3ens_1chain "AB"
d_4ens_1chain "B"
d_5ens_1chain "BA"
d_6ens_1chain "BB"
d_7ens_1chain "C"
d_8ens_1chain "CA"
d_9ens_1chain "CB"
d_10ens_1chain "D"
d_11ens_1chain "DA"
d_12ens_1chain "DB"
d_13ens_1chain "E"
d_14ens_1chain "EA"
d_15ens_1chain "EB"
d_16ens_1chain "F"
d_17ens_1chain "FA"
d_18ens_1chain "FB"
d_19ens_1chain "G"
d_20ens_1chain "GA"
d_21ens_1chain "GB"
d_22ens_1chain "H"
d_23ens_1chain "HA"
d_24ens_1chain "HB"
d_25ens_1chain "I"
d_26ens_1chain "IA"
d_27ens_1chain "J"
d_28ens_1chain "JA"
d_29ens_1chain "K"
d_30ens_1chain "KA"
d_31ens_1chain "L"
d_32ens_1chain "LA"
d_33ens_1chain "M"
d_34ens_1chain "MA"
d_35ens_1chain "N"
d_36ens_1chain "NA"
d_37ens_1chain "PA"
d_38ens_1chain "OA"
d_39ens_1chain "V"
d_40ens_1chain "A"
d_41ens_1chain "Q"
d_42ens_1chain "QA"
d_43ens_1chain "R"
d_44ens_1chain "RA"
d_45ens_1chain "S"
d_46ens_1chain "SA"
d_47ens_1chain "T"
d_48ens_1chain "P"
d_49ens_1chain "U"
d_50ens_1chain "UA"
d_51ens_1chain "O"
d_52ens_1chain "VA"
d_53ens_1chain "W"
d_54ens_1chain "WA"
d_55ens_1chain "X"
d_56ens_1chain "XA"
d_57ens_1chain "Y"
d_58ens_1chain "YA"
d_59ens_1chain "Z"
d_60ens_1chain "ZA"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 265 / Label seq-ID: 1 - 265

Dom-IDAuth asym-IDLabel asym-ID
d_1TATA
d_2AAAA
d_3ABAB
d_4BC
d_5BABA
d_6BBBB
d_7CD
d_8CACA
d_9CBCB
d_10DE
d_11DADA
d_12DBDB
d_13EF
d_14EAEA
d_15EBEB
d_16FG
d_17FAFA
d_18FBFB
d_19GH
d_20GAGA
d_21GBGB
d_22HI
d_23HAHA
d_24HBHB
d_25IJ
d_26IAIA
d_27JK
d_28JAJA
d_29KL
d_30KAKA
d_31LM
d_32LALA
d_33MN
d_34MAMA
d_35NO
d_36NANA
d_37PAPA
d_38OAOA
d_39VV
d_40AB
d_41QR
d_42QAQA
d_43RS
d_44RARA
d_45ST
d_46SASA
d_47TU
d_48PQ
d_49UA
d_50UAUA
d_51OP
d_52VAVA
d_53WW
d_54WAWA
d_55XX
d_56XAXA
d_57YY
d_58YAYA
d_59ZZ
d_60ZAZA

NCS oper:
IDCodeMatrixVector
1given(-0.309011984419, 0.80901407277, -0.500007823485), (-0.809015112627, -0.500001055001, -0.309020213804), (-0.500006140989, 0.309022936138, 0.809010929416)287.817457799, 753.521828509, 109.940187715
2given(0.309008797752, 0.809016221753, 0.500006315813), (0.809013965148, -0.499999218823, 0.309026188811), (0.500009967008, 0.309020281076, -0.809009578915)-177.879786723, 109.937605273, 287.813610304
3given(0.50000887187, 0.309021055718, -0.809009959873), (0.309008464095, 0.809016367514, 0.500006286173), (0.809014769438, -0.499998504215, 0.309025239444)287.813513154, -177.878911797, 109.936986989
4given(-0.809014584833, 0.49999865023, -0.309025486483), (-0.500009213406, -0.309021066862, 0.80900974453), (0.309008394767, 0.809016273016, 0.500006481917)465.701976355, 287.827300748, -177.878732664
5given(0.309009393804, 0.809016330504, -0.500005771486), (0.809014508796, -0.499999043294, -0.30902504957), (-0.500008719021, -0.309020280376, -0.809010350502)109.943046293, 287.823863338, 753.524091638
6given(-0.500008966234, -0.309019655611, -0.809010436355), (0.309009311326, 0.809016673183, -0.500005267998), (0.809014387511, -0.499998874957, -0.309025639457)753.523658432, 109.943642031, 287.823765458
7given(-0.809014535768, 0.499998669847, 0.309025583193), (0.500008953257, 0.309020100826, 0.809010274316), (0.309008944174, 0.809016629889, -0.500005564953)287.815455103, -177.883168692, 109.943683081
8given(-0.500006860373, 0.309023356527, -0.809010324224), (0.309010583596, -0.80901440392, -0.500008153409), (-0.809015203075, -0.50000025937, 0.309021264355)575.636583512, 575.646309049, 575.638295768
9given(-0.809015260961, -0.500000445892, 0.309020811013), (-0.500006626883, 0.309023630302, -0.809010363956), (0.309010809851, -0.809014184068, -0.500008369302)575.638121706, 575.637216763, 575.645879919
10given(-0.309010485491, 0.809014063915, 0.500008764167), (0.809015246244, 0.50000040535, -0.309020915139), (-0.500006851154, 0.309024010453, -0.809010080136)-0.00667428890074, 0.00220387324987, 575.636949988
11given(1, 5.70836094974E-7, 7.52130841145E-8), (5.70836111561E-7, -1, -2.20543363416E-7), (7.52129582204E-8, 2.2054340635E-7, -1)-0.000881979951089, 575.640643603, 575.6399091
12given(-2.00583939014E-7, 3.67328920503E-7, -1), (1, 1.25281020003E-7, -2.0058389294E-7), (1.2528094645E-7, -1, -3.67328945705E-7)575.639581666, 2.69085311402E-5, 575.640462897
13given(1.22687855875E-7, -1, -2.68095870004E-7), (1.296683384E-7, 2.68095885492E-7, -1), (1, 1.22687821458E-7, 1.29668371152E-7)575.6400352, 575.640286178, -0.000468717730826
14given(0.500006140966, -0.309022936144, -0.809010929428), (0.309011984411, -0.809014072779, 0.500007823474), (-0.809015112644, -0.500001054981, -0.309020213791)465.6998123, 287.82154221, 753.521828506
15given(-0.809015112628, -0.500001055007, -0.309020213791), (0.500006140976, -0.309022936129, -0.809010929427), (0.309011984437, -0.809014072769, 0.500007823475)753.521828507, 465.700812291, 287.821542197
16given(0.309011984448, -0.809014072768, 0.500007823469), (-0.809015112628, -0.500001055012, -0.309020213783), (0.500006140969, -0.309022936123, -0.809010929434)287.820542194, 753.522828506, 465.700812294
17given(-0.309008279959, -0.809016282562, -0.500006537424), (0.809014599365, -0.499998591495, 0.30902554347), (-0.500009260845, -0.309021136904, 0.809009688456)753.51850913, 109.937767989, 287.826745768
18given(-0.500010196632, -0.309021024085, 0.809009153185), (-0.309008538086, -0.80901583531, -0.500007101557), (0.80901392241, -0.499999384891, 0.309026032002)287.82692273, 753.519515383, 109.937730236
19given(0.809014713205, -0.499998681848, 0.309025099253), (-0.500008959656, -0.309021365159, 0.809009787418), (-0.309008469272, -0.809016139533, -0.500006651849)109.937076742, 287.827033741, 753.51906609
20given(-0.309009033955, -0.809016435062, 0.500005824701), (0.809014254884, -0.499998998146, -0.309025787349), (0.500009352241, 0.309020079692, 0.809010035796)465.695671263, 287.825060115, -177.883818498
21given(0.500008527406, 0.309019491649, 0.809010770202), (-0.309010111227, -0.809016447773, 0.500005138366), (0.809014353198, -0.499999341014, -0.309024975212)-177.883909045, 465.697003041, 287.824482436
22given(0.809014143364, -0.499999472183, -0.30902531232), (0.500009108808, 0.309019918995, 0.809010247632), (-0.309009719826, -0.809016203473, 0.500005775539)287.824383302, -177.883362699, 465.696209727
23given(0.500006298365, -0.309023557728, 0.809010594717), (0.309010714249, -0.809014413493, -0.500008057174), (0.809015500515, 0.500000119529, -0.309020711922)0.00225435686502, 575.646820701, 0.00211309395024
24given(0.809015143598, 0.50000089744, -0.309020387659), (0.500006614553, -0.309023975748, 0.809010239623), (0.309011137069, -0.809013773042, -0.500008832118)0.0015696479627, 0.00315299837359, 575.646425563
25given(0.309010499267, -0.809014697877, -0.500007729903), (0.8090155437, 0.499999834965, -0.309021059294), (0.500006361355, -0.309023273645, 0.8090106643)575.646256511, 0.00268038209953, 0.00249539307902
26given(6.19311284034E-7, -1.10734980296E-7, -1), (-1, 1.93819062355E-7, -6.19311305516E-7), (1.93819131133E-7, 1, -1.10734860503E-7)575.638690292, 575.6409499, -0.000439067067816
27given(8.35441883229E-7, -1, -1.61877183324E-7), (1.73953036919E-7, -1.61877038218E-7, 1), (-1, -8.3544191154E-7, 1.73952901417E-7)575.639725754, 0.00118121608301, 575.639782438
28given(-0.809015112627, -0.500001055, -0.309020213803), (-0.500006140988, 0.309022936138, 0.809010929416), (-0.30901198442, 0.80901407277, -0.500007823484)753.520828509, 109.940187714, 287.818457799
29given(0.309011984439, -0.809014072769, 0.500007823474), (0.809015112628, 0.500001055008, 0.30902021379), (-0.500006140975, 0.309022936128, 0.809010929428)287.821542196, -177.880828507, 109.939187709
30given(-0.500010065488, -0.309021567681, 0.809009026599), (0.309007812087, 0.809015998128, 0.50000728679), (-0.809014280764, 0.49999878548, -0.309026063688)287.827275296, -177.878312233, 465.702358299
31given(0.809014330087, -0.499998933395, 0.309025695238), (0.500009538289, 0.309020912715, -0.809009602616), (0.309008536019, 0.80901615689, 0.500006582515)109.936755932, 287.814022985, -177.879403813
32given(0.500009097365, 0.309019804772, 0.809010298334), (0.309010335027, 0.809015898222, -0.500005889235), (-0.809013915455, 0.500000036682, 0.309024995621)-177.883791101, 109.943807659, 287.815376161
33given(0.809014031092, -0.499999790628, -0.309025091001), (-0.500008836894, -0.309019271261, -0.809010663105), (0.309010453745, 0.809016254077, -0.500005240087)287.823584164, 753.524307847, 109.942965432
34given(0.809015318316, 0.500000021639, -0.309021347306), (-0.500006720068, 0.309023156697, -0.809010487269), (-0.30901050891, 0.809014627177, 0.500007838336)0.00166107547494, 575.637638587, -0.0062139971393
35given(0.309010823147, -0.809014120736, -0.500008463556), (-0.809015329062, -0.500000448023, 0.309020629279), (-0.500006508478, 0.309023792655, -0.809010375121)575.64550111, 575.638972639, 575.636681547
36given(-0.500006140973, 0.309022936131, 0.809010929428), (-0.309011984433, 0.809014072771, -0.500007823474), (-0.809015112631, -0.500001055002, -0.30902021379)109.939187707, 287.818457801, 753.521828507
37given(-1, -2.13001055625E-8, 1.97368749139E-7), (-2.13001686738E-8, 1, -3.19763355598E-7), (-1.97368742328E-7, -3.19763359801E-7, -1)575.639944991, 0.000107045244192, 575.639383444
38given(-0.30901198442, 0.809014072769, -0.500007823485), (0.809015112626, 0.500001055002, 0.309020213804), (0.500006140989, -0.309022936137, -0.809010929416)287.8184578, -177.881828509, 465.700812285
39given(0.809015112628, 0.500001055007, 0.309020213791), (-0.500006140976, 0.309022936129, 0.809010929427), (0.309011984437, -0.809014072769, 0.500007823475)-177.881828507, 109.939187709, 287.821542197
40given(0.500009371756, 0.309021033316, -0.809009659475), (-0.309008390495, -0.809016235903, -0.500006544606), (-0.809014488597, 0.499998731012, -0.30902560772)287.812215425, 753.519490103, 465.703215812
41given(0.309008631702, 0.809016046299, 0.50000670232), (-0.809014051856, 0.499999210248, -0.309025975689), (-0.500009929335, -0.309020754291, 0.809009421444)-177.879161367, 465.702482455, 287.827214276
42given(-0.500009211989, -0.309019690554, -0.809010271119), (-0.309009156663, -0.809016653301, 0.50000539575), (-0.809014294697, 0.49999888553, 0.309025865333)753.522714406, 465.697209719, 287.815993877
43given(0.309008953119, 0.809016449564, -0.500005851192), (-0.8090141676, 0.49999901225, 0.309025993035), (0.500009543423, 0.309020018904, 0.809009940855)109.943403252, 287.815882184, -177.883558393
44given(-0.809015306476, -0.500000556336, 0.309020513155), (0.500006490272, -0.309023873747, 0.809010355398), (-0.309010911738, 0.809014022819, 0.500008567236)575.637351928, 0.00413182148054, -0.00621868523945
45given(-0.500006242823, 0.309023520705, -0.809010643186), (-0.309011114012, 0.809014210523, 0.500008138523), (0.80901538215, 0.500000470822, -0.309020453405)575.636673709, -0.00550383187596, 0.00159444528015
46given(-9.07550251616E-7, 0.999999999999, 5.9580135181E-7), (4.70459793345E-7, -5.95800925041E-7, 1), (0.999999999999, 9.07550531726E-7, -4.70459252888E-7)-0.00062883848824, 0.000377516525077, 0.000288979918082
47given(0.809015112628, 0.500001055007, 0.309020213791), (0.500006140976, -0.309022936129, -0.809010929427), (-0.309011984437, 0.809014072769, -0.500007823475)-177.882828507, 465.700812291, 287.818457803
48given(2.00608762935E-7, -3.67336256912E-7, 1), (-1, -1.25276706564E-7, 2.0060871736E-7), (1.25276632457E-7, -1, -3.67336282503E-7)0.000418325958549, 575.639973083, 575.640462901
49given(0.500006140975, -0.30902293613, -0.809010929427), (-0.309011984435, 0.80901407277, -0.500007823475), (0.809015112629, 0.500001055005, 0.309020213791)465.700812292, 287.819457802, -177.881828507
50given(-4.25522713288E-7, -2.71050950351E-7, 1), (1, 2.81990972351E-7, 4.25522789615E-7), (-2.81991087925E-7, 1, 2.71050830225E-7)-0.000170524399323, 0.000595502201179, -0.000372333379914
51given(-0.309008662284, -0.809016127583, -0.500006551901), (-0.809013881297, 0.499999277103, -0.309026314035), (0.500010186399, 0.309020433317, -0.809009385168)753.518851325, 465.703435651, 287.812403199
52given(-0.809014307276, 0.499998751049, -0.30902604999), (0.500009780356, 0.30902091275, -0.809009452993), (-0.309008204052, -0.809016269572, -0.500006605353)465.702853323, 287.812771332, 753.519096647
53given(-0.309009636399, -0.809016392645, 0.500005521013), (-0.809014625319, 0.499999025537, 0.30902477325), (-0.500008380562, -0.309020146419, -0.809010610854)465.69658712, 287.816786844, 753.523077534
54given(-0.80901397523, 0.500000018192, 0.30902486905), (-0.500009043394, -0.309020024765, -0.80901024766), (-0.309010265861, -0.809015825619, 0.500006049454)287.815390684, 753.52347978, 465.696914547
55given(0.500006572753, -0.309023453049, 0.809010465117), (-0.309010633573, 0.809014423241, 0.500008091261), (-0.809015361747, -0.500000168453, 0.309020996057)0.00320412503538, -0.00593261836008, 575.63754438
56given(-0.309010947793, 0.80901439264, 0.500007946583), (-0.809015382227, -0.50000029473, 0.309020738123), (0.500006345425, -0.309023328846, 0.80901065306)-0.00652610340336, 575.638017549, 0.00352931842536
57given(-1, -1.76153287809E-7, -3.70189876587E-7), (1.76153226882E-7, -1, 1.64581547609E-7), (-3.70189905578E-7, 1.64581482399E-7, 1)575.639358256, 575.640677818, 0.000880256555092
58given(-1.65889686432E-7, 1, 5.27151789165E-7), (1.36713866339E-8, 5.27151790886E-7, -1), (-1, -1.65889678716E-7, -1.36714746191E-8)-0.000895484994544, 575.639453791, 575.640444973
59given(-0.500006140977, 0.309022936129, 0.809010929426), (0.309011984436, -0.809014072769, 0.500007823476), (0.809015112628, 0.500001055007, 0.309020213792)109.938187709, 287.821542197, -177.881828507

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Components

#1: Protein ...
Type 1 encapsulin shell protein / Maritimacin / Thermotoga bacteriocin


Mass: 30516.787 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: enc, TM_0785 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9WZP2, Hydrolases; Acting on peptide bonds (peptidases)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Thermotoga maritima encapsulin shell
Type: COMPLEX
Details: Thermotoga maritima encapsulin shell expressed by E. coli
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Thermotoga maritima (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 46110 / Num. of class averages: 7 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 180.27 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0016131700
ELECTRON MICROSCOPYf_angle_d0.4263177780
ELECTRON MICROSCOPYf_chiral_restr0.039819620
ELECTRON MICROSCOPYf_plane_restr0.002722980
ELECTRON MICROSCOPYf_dihedral_angle_d3.660917340
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2TATAELECTRON MICROSCOPYNCS constraints1.32444887195E-12
ens_1d_3TATAELECTRON MICROSCOPYNCS constraints1.83089075544E-12
ens_1d_4TATAELECTRON MICROSCOPYNCS constraints1.11310781413E-12
ens_1d_5TATAELECTRON MICROSCOPYNCS constraints9.53537101472E-13
ens_1d_6TATAELECTRON MICROSCOPYNCS constraints1.52106038821E-12
ens_1d_7TATAELECTRON MICROSCOPYNCS constraints1.09673236486E-12
ens_1d_8TATAELECTRON MICROSCOPYNCS constraints2.70061705798E-12
ens_1d_9TATAELECTRON MICROSCOPYNCS constraints3.16782709146E-10
ens_1d_10TATAELECTRON MICROSCOPYNCS constraints2.86542321253E-12
ens_1d_11TATAELECTRON MICROSCOPYNCS constraints8.87214740216E-13
ens_1d_12TATAELECTRON MICROSCOPYNCS constraints9.51078441791E-13
ens_1d_13TATAELECTRON MICROSCOPYNCS constraints4.46091845E-12
ens_1d_14TATAELECTRON MICROSCOPYNCS constraints4.20430956174E-11
ens_1d_15TATAELECTRON MICROSCOPYNCS constraints1.15001610285E-12
ens_1d_16TATAELECTRON MICROSCOPYNCS constraints1.16161538618E-12
ens_1d_17TATAELECTRON MICROSCOPYNCS constraints1.29484521696E-12
ens_1d_18TATAELECTRON MICROSCOPYNCS constraints1.67434703889E-12
ens_1d_19TATAELECTRON MICROSCOPYNCS constraints2.10266684247E-10
ens_1d_20TATAELECTRON MICROSCOPYNCS constraints2.23882182616E-11
ens_1d_21TATAELECTRON MICROSCOPYNCS constraints6.88422098419E-12
ens_1d_22TATAELECTRON MICROSCOPYNCS constraints2.29675325773E-10
ens_1d_23TATAELECTRON MICROSCOPYNCS constraints1.84213781758E-12
ens_1d_24TATAELECTRON MICROSCOPYNCS constraints1.40814237308E-12
ens_1d_25TATAELECTRON MICROSCOPYNCS constraints1.31817494761E-10
ens_1d_26TATAELECTRON MICROSCOPYNCS constraints9.80219038835E-13
ens_1d_27TATAELECTRON MICROSCOPYNCS constraints8.51186255666E-13
ens_1d_28TATAELECTRON MICROSCOPYNCS constraints1.38645583761E-12
ens_1d_29TATAELECTRON MICROSCOPYNCS constraints3.26102155651E-10
ens_1d_30TATAELECTRON MICROSCOPYNCS constraints1.40070526651E-12
ens_1d_31TATAELECTRON MICROSCOPYNCS constraints1.3390015024E-12
ens_1d_32TATAELECTRON MICROSCOPYNCS constraints1.63998372479E-12
ens_1d_33TATAELECTRON MICROSCOPYNCS constraints9.69962337327E-11
ens_1d_34TATAELECTRON MICROSCOPYNCS constraints1.51619970812E-12
ens_1d_35TATAELECTRON MICROSCOPYNCS constraints1.08954972846E-10
ens_1d_36TATAELECTRON MICROSCOPYNCS constraints1.30261399381E-12
ens_1d_37TATAELECTRON MICROSCOPYNCS constraints9.89243372943E-12
ens_1d_38TATAELECTRON MICROSCOPYNCS constraints1.07288411288E-12
ens_1d_39TATAELECTRON MICROSCOPYNCS constraints3.08506834081E-11
ens_1d_40TATAELECTRON MICROSCOPYNCS constraints1.37859140863E-12
ens_1d_41TATAELECTRON MICROSCOPYNCS constraints1.04691967235E-12
ens_1d_42TATAELECTRON MICROSCOPYNCS constraints1.28531178719E-12
ens_1d_43TATAELECTRON MICROSCOPYNCS constraints4.128918505E-11
ens_1d_44TATAELECTRON MICROSCOPYNCS constraints8.08399343142E-13
ens_1d_45TATAELECTRON MICROSCOPYNCS constraints2.24146188278E-11
ens_1d_46TATAELECTRON MICROSCOPYNCS constraints2.16021967116E-10
ens_1d_47TATAELECTRON MICROSCOPYNCS constraints1.37516350782E-11
ens_1d_48TATAELECTRON MICROSCOPYNCS constraints1.03572986338E-12
ens_1d_49TATAELECTRON MICROSCOPYNCS constraints9.65189535189E-13
ens_1d_50TATAELECTRON MICROSCOPYNCS constraints9.26725016635E-13
ens_1d_51TATAELECTRON MICROSCOPYNCS constraints1.03048112814E-12
ens_1d_52TATAELECTRON MICROSCOPYNCS constraints1.14371884761E-12
ens_1d_53TATAELECTRON MICROSCOPYNCS constraints1.06062912781E-12
ens_1d_54TATAELECTRON MICROSCOPYNCS constraints2.28466091456E-10
ens_1d_55TATAELECTRON MICROSCOPYNCS constraints1.34073008978E-12
ens_1d_56TATAELECTRON MICROSCOPYNCS constraints1.06837268272E-12
ens_1d_57TATAELECTRON MICROSCOPYNCS constraints6.19720739478E-11
ens_1d_58TATAELECTRON MICROSCOPYNCS constraints9.20367343286E-13
ens_1d_59TATAELECTRON MICROSCOPYNCS constraints8.38508388114E-13
ens_1d_60TATAELECTRON MICROSCOPYNCS constraints1.46919232525E-11

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