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- PDB-3ia0: Ethanolamine Utilization Microcompartment Shell Subunit, EutS-G39... -

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Basic information

Entry
Database: PDB / ID: 3ia0
TitleEthanolamine Utilization Microcompartment Shell Subunit, EutS-G39V mutant
ComponentsEthanolamine utilization protein eutS
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / protein hexamerization / structural molecule activity / identical protein binding
Similarity search - Function
Bacterial microcompartment shell protein EutS/PduU/CutR / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartment shell protein EutS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsTanaka, S. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Science / Year: 2010
Title: Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli.
Authors: Tanaka, S. / Sawaya, M.R. / Yeates, T.O.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 11, 2016Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ethanolamine utilization protein eutS
B: Ethanolamine utilization protein eutS
C: Ethanolamine utilization protein eutS
D: Ethanolamine utilization protein eutS
E: Ethanolamine utilization protein eutS
F: Ethanolamine utilization protein eutS
G: Ethanolamine utilization protein eutS
H: Ethanolamine utilization protein eutS
I: Ethanolamine utilization protein eutS
J: Ethanolamine utilization protein eutS
K: Ethanolamine utilization protein eutS
L: Ethanolamine utilization protein eutS
M: Ethanolamine utilization protein eutS
N: Ethanolamine utilization protein eutS
O: Ethanolamine utilization protein eutS
P: Ethanolamine utilization protein eutS
Q: Ethanolamine utilization protein eutS
R: Ethanolamine utilization protein eutS
S: Ethanolamine utilization protein eutS
T: Ethanolamine utilization protein eutS
U: Ethanolamine utilization protein eutS
V: Ethanolamine utilization protein eutS
W: Ethanolamine utilization protein eutS
X: Ethanolamine utilization protein eutS
Y: Ethanolamine utilization protein eutS
Z: Ethanolamine utilization protein eutS
a: Ethanolamine utilization protein eutS
b: Ethanolamine utilization protein eutS
c: Ethanolamine utilization protein eutS
d: Ethanolamine utilization protein eutS
e: Ethanolamine utilization protein eutS
f: Ethanolamine utilization protein eutS
g: Ethanolamine utilization protein eutS
h: Ethanolamine utilization protein eutS
i: Ethanolamine utilization protein eutS
j: Ethanolamine utilization protein eutS
k: Ethanolamine utilization protein eutS
l: Ethanolamine utilization protein eutS
m: Ethanolamine utilization protein eutS
n: Ethanolamine utilization protein eutS
o: Ethanolamine utilization protein eutS
p: Ethanolamine utilization protein eutS
q: Ethanolamine utilization protein eutS
r: Ethanolamine utilization protein eutS
s: Ethanolamine utilization protein eutS
t: Ethanolamine utilization protein eutS
u: Ethanolamine utilization protein eutS
v: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)613,18848
Polymers613,18848
Non-polymers00
Water0
1
A: Ethanolamine utilization protein eutS
B: Ethanolamine utilization protein eutS
C: Ethanolamine utilization protein eutS
D: Ethanolamine utilization protein eutS
E: Ethanolamine utilization protein eutS
F: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-89 kcal/mol
Surface area23430 Å2
MethodPISA
2
G: Ethanolamine utilization protein eutS
H: Ethanolamine utilization protein eutS
I: Ethanolamine utilization protein eutS
J: Ethanolamine utilization protein eutS
K: Ethanolamine utilization protein eutS
L: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18730 Å2
ΔGint-89 kcal/mol
Surface area23410 Å2
MethodPISA
3
M: Ethanolamine utilization protein eutS
N: Ethanolamine utilization protein eutS
O: Ethanolamine utilization protein eutS
P: Ethanolamine utilization protein eutS
Q: Ethanolamine utilization protein eutS
R: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18770 Å2
ΔGint-89 kcal/mol
Surface area23390 Å2
MethodPISA
4
S: Ethanolamine utilization protein eutS
T: Ethanolamine utilization protein eutS
U: Ethanolamine utilization protein eutS
V: Ethanolamine utilization protein eutS
W: Ethanolamine utilization protein eutS
X: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18770 Å2
ΔGint-89 kcal/mol
Surface area23380 Å2
MethodPISA
5
Y: Ethanolamine utilization protein eutS
Z: Ethanolamine utilization protein eutS
a: Ethanolamine utilization protein eutS
b: Ethanolamine utilization protein eutS
c: Ethanolamine utilization protein eutS
d: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18760 Å2
ΔGint-89 kcal/mol
Surface area23390 Å2
MethodPISA
6
e: Ethanolamine utilization protein eutS
f: Ethanolamine utilization protein eutS
g: Ethanolamine utilization protein eutS
h: Ethanolamine utilization protein eutS
i: Ethanolamine utilization protein eutS
j: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18800 Å2
ΔGint-89 kcal/mol
Surface area23350 Å2
MethodPISA
7
k: Ethanolamine utilization protein eutS
l: Ethanolamine utilization protein eutS
m: Ethanolamine utilization protein eutS
n: Ethanolamine utilization protein eutS
o: Ethanolamine utilization protein eutS
p: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-89 kcal/mol
Surface area23420 Å2
MethodPISA
8
q: Ethanolamine utilization protein eutS
r: Ethanolamine utilization protein eutS
s: Ethanolamine utilization protein eutS
t: Ethanolamine utilization protein eutS
u: Ethanolamine utilization protein eutS
v: Ethanolamine utilization protein eutS


Theoretical massNumber of molelcules
Total (without water)76,6496
Polymers76,6496
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-89 kcal/mol
Surface area23410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.581, 151.394, 127.456
Angle α, β, γ (deg.)90.000, 90.390, 90.000
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T
211U
221V
231W
241X
251Y
261Z
271a
281b
291c
301d
311e
321f
331g
341h
351i
361j
371k
381l
391m
401n
411o
421p
431q
441r
451s
461t
471u
481v

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 3 - 113 / Label seq-ID: 3 - 113

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 3:113 )AA
2chain B and (resseq 3:113 )BB
3chain C and (resseq 3:113 )CC
4chain D and (resseq 3:113 )DD
5chain E and (resseq 3:113 )EE
6chain F and (resseq 3:113 )FF
7chain G and (resseq 3:113 )GG
8chain H and (resseq 3:113 )HH
9chain I and (resseq 3:113 )II
10chain J and (resseq 3:113 )JJ
11chain K and (resseq 3:113 )KK
12chain L and (resseq 3:113 )LL
13chain M and (resseq 3:113 )MM
14chain N and (resseq 3:113 )NN
15chain O and (resseq 3:113 )OO
16chain P and (resseq 3:113 )PP
17chain Q and (resseq 3:113 )QQ
18chain R and (resseq 3:113 )RR
19chain S and (resseq 3:113 )SS
20chain T and (resseq 3:113 )TT
21chain U and (resseq 3:113 )UU
22chain V and (resseq 3:113 )VV
23chain W and (resseq 3:113 )WW
24chain X and (resseq 3:113 )XX
25chain Y and (resseq 3:113 )YY
26chain Z and (resseq 3:113 )ZZ
27chain a and (resseq 3:113 )aAA
28chain b and (resseq 3:113 )bBA
29chain c and (resseq 3:113 )cCA
30chain d and (resseq 3:113 )dDA
31chain e and (resseq 3:113 )eEA
32chain f and (resseq 3:113 )fFA
33chain g and (resseq 3:113 )gGA
34chain h and (resseq 3:113 )hHA
35chain i and (resseq 3:113 )iIA
36chain j and (resseq 3:113 )jJA
37chain k and (resseq 3:113 )kKA
38chain l and (resseq 3:113 )lLA
39chain m and (resseq 3:113 )mMA
40chain n and (resseq 3:113 )nNA
41chain o and (resseq 3:113 )oOA
42chain p and (resseq 3:113 )pPA
43chain q and (resseq 3:113 )qQA
44chain r and (resseq 3:113 )rRA
45chain s and (resseq 3:113 )sSA
46chain t and (resseq 3:113 )tTA
47chain u and (resseq 3:113 )uUA
48chain v and (resseq 3:113 )vVA

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.505098, 0.06314, -0.860749), (-0.163952, 0.98618, -0.023868), (0.847346, 0.153177, 0.508469)26.686001, 5.10663, -16.4326
3given(-0.489439, -0.027678, -0.871598), (-0.275136, 0.953346, 0.124227), (0.827496, 0.30061, -0.47422)54.798901, 5.88096, -1.00632
4given(-0.97743, -0.210181, -0.021335), (-0.207582, 0.936731, 0.281859), (-0.039256, 0.279926, -0.959219)55.649399, 1.49664, 30.5763
5given(-0.480658, -0.286202, 0.828889), (-0.025784, 0.949444, 0.312876), (-0.876529, 0.129014, -0.463737)28.992599, -3.93242, 46.559101
6given(0.512745, -0.18344, 0.838715), (0.075022, 0.982743, 0.169077), (-0.855257, -0.023772, 0.517659)0.975197, -4.59264, 31.2642
7given(-0.50361, -0.165796, 0.847873), (0.15851, 0.94702, 0.279333), (-0.849265, 0.275071, -0.450648)67.363297, 13.7581, -11.769
8given(0.485054, -0.251892, 0.83742), (0.265188, 0.954893, 0.133624), (-0.833305, 0.157259, 0.529973)71.972504, 7.12742, 36.812199
9given(0.978248, -0.206003, -0.024379), (0.205211, 0.978212, -0.031474), (0.030332, 0.025787, 0.999207)31.816799, -1.23902, 64.362
10given(0.482066, -0.058241, -0.874197), (0.026019, 0.9983, -0.052162), (0.875749, 0.0024, 0.482761)-12.5714, -3.1583, 43.287701
11given(-0.510845, 0.041552, -0.858668), (-0.076565, 0.992663, 0.093587), (0.856257, 0.113553, -0.503915)-17.0366, 3.45446, -5.53554
12given(-0.999902, -0.013869, 0.001774), (-0.01295, 0.966494, 0.256361), (-0.00527, 0.256313, -0.96658)22.8853, 11.7502, -32.958801
13given(0.518655, 0.190773, -0.833429), (0.080743, -0.981361, -0.174387), (-0.851163, 0.023153, -0.524391)-11.4543, -67.974503, -25.021799
14given(0.999896, -0.00092, 0.014413), (-0.00065, -0.999825, -0.018719), (0.014428, 0.018708, -0.999721)36.9646, -59.503101, -49.523102
15given(0.494956, -0.067678, 0.866278), (-0.17531, -0.984238, 0.023271), (0.851049, -0.163385, -0.499019)84.810204, -57.184101, -20.378599
16given(-0.495055, 0.03365, 0.86821), (-0.279767, -0.952205, -0.122618), (0.822588, -0.3036, 0.480809)82.918404, -65.772903, 35.639
17given(-0.976284, 0.216062, 0.013659), (-0.211323, -0.937366, -0.276923), (-0.04703, -0.273242, 0.960795)33.4062, -74.450302, 61.796001
18given(-0.472668, 0.284476, -0.834061), (-0.017716, -0.949339, -0.313754), (-0.881062, -0.133525, 0.453762)-14.0596, -75.996002, 29.9084
19given(-0.496824, 0.160322, -0.852914), (0.168594, -0.946236, -0.27607), (-0.851318, -0.280954, 0.443084)51.712898, -61.893101, 25.383801
20given(0.483113, 0.259999, -0.836064), (0.28152, -0.950314, -0.132854), (-0.829065, -0.171185, -0.532304)27.133499, -65.3433, 29.829
21given(0.977068, 0.209559, 0.037712), (0.208894, -0.977716, 0.02084), (0.041239, -0.012484, -0.999071)9.89582, -64.5065, 11.5913
22given(0.475852, 0.055244, 0.877789), (0.02828, -0.99847, 0.047509), (0.879071, 0.002217, -0.476686)17.614201, -60.127701, -12.9936
23given(-0.518752, -0.043243, 0.85383), (-0.074495, -0.992635, -0.095533), (0.851673, -0.113164, 0.51171)42.8195, -56.783798, -17.465599
24given(-0.999829, 0.010809, -0.015035), (-0.006726, -0.968476, -0.249015), (-0.017253, -0.248872, 0.968383)59.736198, -57.734402, 2.17536
25given(-0.518941, 0.195406, 0.832176), (-0.08546, -0.980504, 0.176942), (0.850528, 0.020705, 0.525523)97.486504, 31.969601, 23.2824
26given(-0.999771, 0.002441, -0.021268), (-0.003023, -0.999621, 0.02738), (-0.021193, 0.027438, 0.999399)58.300598, 19.393801, 82.962799
27given(-0.492781, -0.072701, -0.867111), (0.177839, -0.983884, -0.018575), (-0.851786, -0.16336, 0.497769)-14.066, 10.1626, 78.884102
28given(0.487107, 0.03583, -0.872607), (0.289957, -0.949117, 0.122889), (-0.823803, -0.312879, -0.472711)-47.5228, 15.5576, 14.6192
29given(0.977278, 0.211701, -0.010487), (0.206254, -0.9384, 0.277244), (0.048851, -0.273107, -0.960742)-7.59037, 28.537399, -47.027302
30given(0.473792, 0.27867, 0.835383), (0.012361, -0.950623, 0.310102), (0.88055, -0.136598, -0.453842)64.8153, 37.1712, -41.369801
31given(0.999908, 0.009101, 0.010104), (0.006132, -0.964938, 0.262405), (0.012137, -0.262319, -0.964905)36.1366, 17.024599, 14.9968
32given(0.504922, 0.16341, 0.847556), (-0.17534, -0.942027, 0.28608), (0.845168, -0.293058, -0.446998)33.307301, 15.3096, 24.608299
33given(-0.484467, 0.263824, 0.834079), (-0.277189, -0.950608, 0.13968), (0.829733, -0.163527, 0.533668)23.4841, 13.9564, 26.952
34given(-0.976497, 0.211705, -0.040421), (-0.21125, -0.977313, -0.015261), (-0.042735, -0.006364, 0.999066)16.0681, 14.2897, 19.4224
35given(-0.478287, 0.053401, -0.876579), (-0.027326, -0.998571, -0.045923), (-0.877778, 0.001989, 0.479063)18.9076, 15.892, 9.87586
36given(0.516448, -0.043895, -0.855193), (0.081153, -0.991682, 0.099908), (-0.852465, -0.120999, -0.508589)28.9643, 17.3549, 7.60698
37given(0.508954, 0.038251, 0.859943), (0.082535, 0.992241, -0.092983), (-0.856827, 0.1183, 0.501848)82.825996, -86.040001, 73.076698
38given(0.999934, -0.011385, 0.001751), (0.01144, 0.963695, -0.26676), (0.001349, 0.266763, 0.963761)0.103685, -96.457603, 75.910301
39given(0.508815, -0.169149, -0.844095), (-0.158715, 0.945267, -0.285095), (0.846119, 0.279031, 0.45412)-45.095402, -91.669296, 7.5483
40given(-0.485136, -0.252163, -0.837291), (-0.264968, 0.954893, -0.134055), (0.833328, 0.15682, -0.530069)-9.37491, -76.782898, -65.731796
41given(-0.978507, -0.203871, 0.030996), (-0.203242, 0.978875, 0.022288), (-0.034885, 0.015509, -0.999271)74.3741, -67.1577, -69.563202
42given(-0.482133, -0.051437, 0.874587), (-0.022085, 0.998671, 0.04656), (-0.875819, 0.003133, -0.482629)119.733002, -71.740997, -0.657814
43given(-0.512996, -0.18669, -0.837844), (-0.07487, 0.982074, -0.172987), (0.85512, -0.026013, -0.517778)21.547501, -78.379799, 10.3853
44given(-0.999968, -0.005151, 0.006145), (-0.00521, 0.99994, -0.009641), (-0.006095, -0.009673, -0.999935)23.352699, -75.966797, -5.56874
45given(-0.502873, 0.07091, 0.861446), (0.169155, 0.985432, 0.017629), (-0.847647, 0.154583, -0.507542)38.348099, -73.183701, -11.801
46given(0.478727, -0.027802, 0.877523), (0.289001, 0.948786, -0.127603), (-0.829035, 0.314693, 0.462244)51.174702, -73.014702, -3.13729
47given(0.977953, -0.207849, 0.020178), (0.204963, 0.936874, -0.283297), (0.039979, 0.281187, 0.95882)49.163399, -75.964302, 14.4507
48given(0.482565, -0.28422, -0.828462), (0.020623, 0.949309, -0.313667), (0.875617, 0.13428, 0.463965)34.3241, -78.413803, 19.3016

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Components

#1: Protein ...
Ethanolamine utilization protein eutS


Mass: 12774.759 Da / Num. of mol.: 48 / Mutation: G39V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2462, eutS, JW2446, ypfE / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P63746

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1M sodium/potassium phosphate, 12% PEG3000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.463
ReflectionResolution: 2.5→60 Å / Num. obs: 173054 / % possible obs: 90.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.166 / Χ2: 1.329 / Net I/σ(I): 4.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.592.60.645176670.57192.7
2.59-2.692.70.553176840.595193.1
2.69-2.822.70.396176990.715192.7
2.82-2.962.70.338176260.821192.3
2.96-3.152.70.267174071.043191.8
3.15-3.392.70.226174211.25191.4
3.39-3.732.80.185172541.748190.5
3.73-4.272.80.155170332.089189.6
4.27-5.382.80.135168042.304188.1
5.38-602.90.109164592.094186.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.2 Å58.88 Å
Translation4.2 Å58.88 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I96

3i96


Resolution: 2.5→58.881 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.756 / σ(F): 0.05 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.239 2011 1.3 %
Rwork0.217 --
obs0.217 154545 80.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 75.988 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 147.98 Å2 / Biso mean: 68.008 Å2 / Biso min: 37.28 Å2
Baniso -1Baniso -2Baniso -3
1--26.763 Å21.573 Å2-0.625 Å2
2--57.742 Å211.539 Å2
3----30.979 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39312 0 0 0 39312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00539840
X-RAY DIFFRACTIONf_angle_d0.92653904
X-RAY DIFFRACTIONf_chiral_restr0.0536624
X-RAY DIFFRACTIONf_plane_restr0.0026816
X-RAY DIFFRACTIONf_dihedral_angle_d15.34414400
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A819X-RAY DIFFRACTIONPOSITIONAL0.027
12B819X-RAY DIFFRACTIONPOSITIONAL0.027
13C819X-RAY DIFFRACTIONPOSITIONAL0.029
14D819X-RAY DIFFRACTIONPOSITIONAL0.03
15E819X-RAY DIFFRACTIONPOSITIONAL0.029
16F819X-RAY DIFFRACTIONPOSITIONAL0.029
17G819X-RAY DIFFRACTIONPOSITIONAL0.028
18H819X-RAY DIFFRACTIONPOSITIONAL0.028
19I819X-RAY DIFFRACTIONPOSITIONAL0.027
110J819X-RAY DIFFRACTIONPOSITIONAL0.028
111K819X-RAY DIFFRACTIONPOSITIONAL0.028
112L819X-RAY DIFFRACTIONPOSITIONAL0.027
113M819X-RAY DIFFRACTIONPOSITIONAL0.028
114N819X-RAY DIFFRACTIONPOSITIONAL0.022
115O819X-RAY DIFFRACTIONPOSITIONAL0.027
116P819X-RAY DIFFRACTIONPOSITIONAL0.028
117Q819X-RAY DIFFRACTIONPOSITIONAL0.03
118R819X-RAY DIFFRACTIONPOSITIONAL0.03
119S819X-RAY DIFFRACTIONPOSITIONAL0.028
120T819X-RAY DIFFRACTIONPOSITIONAL0.029
121U819X-RAY DIFFRACTIONPOSITIONAL0.027
122V819X-RAY DIFFRACTIONPOSITIONAL0.027
123W819X-RAY DIFFRACTIONPOSITIONAL0.029
124X819X-RAY DIFFRACTIONPOSITIONAL0.027
125Y819X-RAY DIFFRACTIONPOSITIONAL0.03
126Z819X-RAY DIFFRACTIONPOSITIONAL0.023
127a819X-RAY DIFFRACTIONPOSITIONAL0.027
128b819X-RAY DIFFRACTIONPOSITIONAL0.029
129c819X-RAY DIFFRACTIONPOSITIONAL0.03
130d819X-RAY DIFFRACTIONPOSITIONAL0.03
131e819X-RAY DIFFRACTIONPOSITIONAL0.026
132f819X-RAY DIFFRACTIONPOSITIONAL0.029
133g819X-RAY DIFFRACTIONPOSITIONAL0.029
134h819X-RAY DIFFRACTIONPOSITIONAL0.028
135i819X-RAY DIFFRACTIONPOSITIONAL0.027
136j819X-RAY DIFFRACTIONPOSITIONAL0.03
137k819X-RAY DIFFRACTIONPOSITIONAL0.027
138l819X-RAY DIFFRACTIONPOSITIONAL0.026
139m819X-RAY DIFFRACTIONPOSITIONAL0.029
140n819X-RAY DIFFRACTIONPOSITIONAL0.028
141o819X-RAY DIFFRACTIONPOSITIONAL0.027
142p819X-RAY DIFFRACTIONPOSITIONAL0.028
143q819X-RAY DIFFRACTIONPOSITIONAL0.028
144r819X-RAY DIFFRACTIONPOSITIONAL0.018
145s819X-RAY DIFFRACTIONPOSITIONAL0.028
146t819X-RAY DIFFRACTIONPOSITIONAL0.031
147u819X-RAY DIFFRACTIONPOSITIONAL0.029
148v819X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.5720.4351130.361106091072267
2.572-2.6550.3951270.356111311125870
2.655-2.750.3911260.303117301185674
2.75-2.860.3171510.308121051225676
2.86-2.990.3461530.284124471260079
2.99-3.1480.3141600.263128751303581
3.148-3.3450.2731480.245131781332683
3.345-3.6020.2131640.225135361370086
3.602-3.9640.231470.2138171396487
3.964-4.5360.1711480.161138391398787
4.536-5.7060.211560.174137181387486
5.706-28.0020.1461360.174135161365285

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