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- PDB-4ubd: Crystal structure of a neutralizing human monoclonal antibody wit... -

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Basic information

Entry
Database: PDB / ID: 4ubd
TitleCrystal structure of a neutralizing human monoclonal antibody with 1968 H3 HA
Components
  • (Hemagglutinin ...) x 2
  • (monoclonal antibody ...) x 2
Keywordsviral protein/immune system / Hemagglutinin / H3N2 / Monoclonal antibody / viral protein-immune system complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins ...Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsShore, D.A. / Yang, H. / Cho, M. / Donis, R.O. / Stevens, J.
CitationJournal: Nat Commun / Year: 2015
Title: A potent broad-spectrum protective human monoclonal antibody crosslinking two haemagglutinin monomers of influenza A virus.
Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. ...Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. / Lee, H. / Shin, J. / Stevens, J. / Hong, S. / Qin, C.F. / Gao, G.F. / Chang, S.J. / Donis, R.O.
History
DepositionAug 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 4, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_assembly ...chem_comp / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_conn
Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
U: Hemagglutinin HA1 chain
V: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
M: Hemagglutinin HA1 chain
Q: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
B: Hemagglutinin HA2 chain
J: Hemagglutinin HA2 chain
N: Hemagglutinin HA2 chain
R: Hemagglutinin HA2 chain
C: monoclonal antibody H chain
D: monoclonal antibody L chain
Y: monoclonal antibody H chain
X: monoclonal antibody L chain
G: monoclonal antibody H chain
H: monoclonal antibody L chain
S: monoclonal antibody H chain
T: monoclonal antibody L chain
O: monoclonal antibody H chain
P: monoclonal antibody L chain
K: monoclonal antibody H chain
L: monoclonal antibody L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)625,69840
Polymers618,38424
Non-polymers7,31416
Water0
1
A: Hemagglutinin HA1 chain
I: Hemagglutinin HA1 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
B: Hemagglutinin HA2 chain
J: Hemagglutinin HA2 chain
C: monoclonal antibody H chain
D: monoclonal antibody L chain
G: monoclonal antibody H chain
H: monoclonal antibody L chain
K: monoclonal antibody H chain
L: monoclonal antibody L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,95020
Polymers309,19212
Non-polymers3,7588
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
U: Hemagglutinin HA1 chain
V: Hemagglutinin HA2 chain
M: Hemagglutinin HA1 chain
Q: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
R: Hemagglutinin HA2 chain
Y: monoclonal antibody H chain
X: monoclonal antibody L chain
S: monoclonal antibody H chain
T: monoclonal antibody L chain
O: monoclonal antibody H chain
P: monoclonal antibody L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,74720
Polymers309,19212
Non-polymers3,5558
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.700, 128.700, 428.319
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21U
12A
22I
13A
23M
14A
24Q
15A
25E
16U
26I
17U
27M
18U
28Q
19U
29E
110V
210F
111V
211B
112V
212J
113V
213N
114V
214R
115I
215M
116I
216Q
117I
217E
118M
218Q
119M
219E
120Q
220E
121F
221B
122F
222J
123F
223N
124F
224R
125B
225J
126B
226N
127B
227R
128J
228N
129J
229R
130N
230R
131C
231Y
132C
232G
133C
233S
134C
234O
135C
235K
136D
236X
137D
237H
138D
238T
139D
239P
140D
240L
141Y
241G
142Y
242S
143Y
243O
144Y
244K
145X
245H
146X
246T
147X
247P
148X
248L
149G
249S
150G
250O
151G
251K
152H
252T
153H
253P
154H
254L
155S
255O
156S
256K
157T
257P
158T
258L
159O
259K
160P
260L

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRAA9 - 3281 - 320
21SERSERTHRTHRUB9 - 3281 - 320
12SERSERPROPROAA9 - 3241 - 316
22SERSERPROPROID9 - 3241 - 316
13SERSERTHRTHRAA9 - 3281 - 320
23SERSERTHRTHRME9 - 3281 - 320
14SERSERTHRTHRAA9 - 3281 - 320
24SERSERTHRTHRQF9 - 3281 - 320
15SERSERTHRTHRAA9 - 3281 - 320
25SERSERTHRTHREG9 - 3281 - 320
16SERSERPROPROUB9 - 3241 - 316
26SERSERPROPROID9 - 3241 - 316
17SERSERTHRTHRUB9 - 3281 - 320
27SERSERTHRTHRME9 - 3281 - 320
18SERSERTHRTHRUB9 - 3281 - 320
28SERSERTHRTHRQF9 - 3281 - 320
19SERSERTHRTHRUB9 - 3281 - 320
29SERSERTHRTHREG9 - 3281 - 320
110ILEILEPHEPHEVC10 - 17110 - 171
210ILEILEPHEPHEFH10 - 17110 - 171
111ILEILEGLNGLNVC10 - 17210 - 172
211ILEILEGLNGLNBI10 - 17210 - 172
112ILEILEPHEPHEVC10 - 17110 - 171
212ILEILEPHEPHEJJ10 - 17110 - 171
113ILEILEPHEPHEVC10 - 17110 - 171
213ILEILEPHEPHENK10 - 17110 - 171
114ILEILEGLNGLNVC10 - 17210 - 172
214ILEILEGLNGLNRL10 - 17210 - 172
115SERSERPROPROID9 - 3241 - 316
215SERSERPROPROME9 - 3241 - 316
116SERSERPROPROID9 - 3241 - 316
216SERSERPROPROQF9 - 3241 - 316
117SERSERPROPROID9 - 3241 - 316
217SERSERPROPROEG9 - 3241 - 316
118SERSERTHRTHRME9 - 3281 - 320
218SERSERTHRTHRQF9 - 3281 - 320
119SERSERTHRTHRME9 - 3281 - 320
219SERSERTHRTHREG9 - 3281 - 320
120SERSERTHRTHRQF9 - 3281 - 320
220SERSERTHRTHREG9 - 3281 - 320
121ILEILEPHEPHEFH10 - 17110 - 171
221ILEILEPHEPHEBI10 - 17110 - 171
122ILEILEPHEPHEFH10 - 17110 - 171
222ILEILEPHEPHEJJ10 - 17110 - 171
123ILEILEGLNGLNFH10 - 17210 - 172
223ILEILEGLNGLNNK10 - 17210 - 172
124ILEILEPHEPHEFH10 - 17110 - 171
224ILEILEPHEPHERL10 - 17110 - 171
125PHEPHEPHEPHEBI9 - 1719 - 171
225PHEPHEPHEPHEJJ9 - 1719 - 171
126ILEILEPHEPHEBI10 - 17110 - 171
226ILEILEPHEPHENK10 - 17110 - 171
127ILEILEGLNGLNBI10 - 17210 - 172
227ILEILEGLNGLNRL10 - 17210 - 172
128ILEILEPHEPHEJJ10 - 17110 - 171
228ILEILEPHEPHENK10 - 17110 - 171
129ILEILEPHEPHEJJ10 - 17110 - 171
229ILEILEPHEPHERL10 - 17110 - 171
130ILEILEPHEPHENK10 - 17110 - 171
230ILEILEPHEPHERL10 - 17110 - 171
131GLNGLNPROPROCM1 - 2261 - 226
231GLNGLNPROPROYO1 - 2261 - 226
132GLNGLNPROPROCM1 - 2261 - 226
232GLNGLNPROPROGQ1 - 2261 - 226
133GLNGLNPROPROCM1 - 2261 - 226
233GLNGLNPROPROSS1 - 2261 - 226
134GLNGLNPROPROCM1 - 2261 - 226
234GLNGLNPROPROOU1 - 2261 - 226
135GLNGLNPROPROCM1 - 2261 - 226
235GLNGLNPROPROKW1 - 2261 - 226
136VALVALGLUGLUDN2 - 2142 - 214
236VALVALGLUGLUXP2 - 2142 - 214
137VALVALGLUGLUDN2 - 2142 - 214
237VALVALGLUGLUHR2 - 2142 - 214
138VALVALGLUGLUDN2 - 2142 - 214
238VALVALGLUGLUTT2 - 2142 - 214
139VALVALGLUGLUDN2 - 2142 - 214
239VALVALGLUGLUPV2 - 2142 - 214
140VALVALGLUGLUDN2 - 2142 - 214
240VALVALGLUGLULX2 - 2142 - 214
141GLNGLNPROPROYO1 - 2261 - 226
241GLNGLNPROPROGQ1 - 2261 - 226
142GLNGLNPROPROYO1 - 2261 - 226
242GLNGLNPROPROSS1 - 2261 - 226
143GLNGLNPROPROYO1 - 2261 - 226
243GLNGLNPROPROOU1 - 2261 - 226
144GLNGLNPROPROYO1 - 2261 - 226
244GLNGLNPROPROKW1 - 2261 - 226
145VALVALGLUGLUXP2 - 2142 - 214
245VALVALGLUGLUHR2 - 2142 - 214
146VALVALGLUGLUXP2 - 2142 - 214
246VALVALGLUGLUTT2 - 2142 - 214
147VALVALGLUGLUXP2 - 2142 - 214
247VALVALGLUGLUPV2 - 2142 - 214
148VALVALGLUGLUXP2 - 2142 - 214
248VALVALGLUGLULX2 - 2142 - 214
149GLNGLNPROPROGQ1 - 2261 - 226
249GLNGLNPROPROSS1 - 2261 - 226
150GLNGLNPROPROGQ1 - 2261 - 226
250GLNGLNPROPROOU1 - 2261 - 226
151GLNGLNPROPROGQ1 - 2261 - 226
251GLNGLNPROPROKW1 - 2261 - 226
152VALVALGLUGLUHR2 - 2142 - 214
252VALVALGLUGLUTT2 - 2142 - 214
153VALVALGLUGLUHR2 - 2142 - 214
253VALVALGLUGLUPV2 - 2142 - 214
154VALVALGLUGLUHR2 - 2142 - 214
254VALVALGLUGLULX2 - 2142 - 214
155GLNGLNPROPROSS1 - 2261 - 226
255GLNGLNPROPROOU1 - 2261 - 226
156GLNGLNPROPROSS1 - 2261 - 226
256GLNGLNPROPROKW1 - 2261 - 226
157VALVALGLUGLUTT2 - 2142 - 214
257VALVALGLUGLUPV2 - 2142 - 214
158VALVALGLUGLUTT2 - 2142 - 214
258VALVALGLUGLULX2 - 2142 - 214
159GLNGLNPROPROOU1 - 2261 - 226
259GLNGLNPROPROKW1 - 2261 - 226
160VALVALGLUGLUPV2 - 2142 - 214
260VALVALGLUGLULX2 - 2142 - 214

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

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Components

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Hemagglutinin ... , 2 types, 12 molecules AUIMQEVFBJNR

#1: Protein
Hemagglutinin HA1 chain


Mass: 35325.730 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#2: Protein
Hemagglutinin HA2 chain


Mass: 20198.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7

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Antibody , 2 types, 12 molecules CYGSOKDXHTPL

#3: Antibody
monoclonal antibody H chain


Mass: 23865.666 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody
monoclonal antibody L chain


Mass: 23674.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 3 types, 16 molecules

#5: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 6 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 3000, 100mM Na Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 94551 / % possible obs: 99.5 % / Redundancy: 3.7 % / Net I/σ(I): 1.7

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→50 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.88 / SU B: 79.459 / SU ML: 0.517 / Cross valid method: THROUGHOUT / ESU R Free: 0.621 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25755 4962 5 %RANDOM
Rwork0.21247 ---
obs0.21469 94551 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 116.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0.3 Å20 Å2
2---0.61 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42604 0 482 0 43086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01944200
X-RAY DIFFRACTIONr_bond_other_d0.0060.0240744
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.95760138
X-RAY DIFFRACTIONr_angle_other_deg1.241393802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98455464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99824.2741963
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.177157139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.00615264
X-RAY DIFFRACTIONr_chiral_restr0.120.26777
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02150142
X-RAY DIFFRACTIONr_gen_planes_other0.0050.0210158
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_it5.4536.50121946
X-RAY DIFFRACTIONr_mcbond_other5.4526.50121945
X-RAY DIFFRACTIONr_mcangle_it8.949.74527380
X-RAY DIFFRACTIONr_mcangle_other8.949.74527381
X-RAY DIFFRACTIONr_scbond_it5.3786.74522254
X-RAY DIFFRACTIONr_scbond_other5.3786.74522252
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other99.99232758
X-RAY DIFFRACTIONr_long_range_B_refined13.93250.78747866
X-RAY DIFFRACTIONr_long_range_B_other13.93250.78847867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A186730.07
12U186730.07
21A183390.07
22I183390.07
31A185270.08
32M185270.08
41A184730.08
42Q184730.08
51A185760.08
52E185760.08
61U184130.07
62I184130.07
71U186280.07
72M186280.07
81U185430.08
82Q185430.08
91U186200.07
92E186200.07
101V86290.1
102F86290.1
111V87340.09
112B87340.09
121V85730.1
122J85730.1
131V85600.11
132N85600.11
141V85780.11
142R85780.11
151I185030.06
152M185030.06
161I183790.07
162Q183790.07
171I184460.06
172E184460.06
181M185160.08
182Q185160.08
191M186630.07
192E186630.07
201Q187770.06
202E187770.06
211F86330.1
212B86330.1
221F85670.1
222J85670.1
231F86460.1
232N86460.1
241F86230.1
242R86230.1
251B87030.09
252J87030.09
261B85710.1
262N85710.1
271B86310.1
272R86310.1
281J86440.09
282N86440.09
291J85960.09
292R85960.09
301N85570.11
302R85570.11
311C123100
312Y123100
321C122690.02
322G122690.02
331C122720.01
332S122720.01
341C122660.01
342O122660.01
351C122770.01
352K122770.01
361D123060
362X123060
371D122390.01
372H122390.01
381D122400.01
382T122400.01
391D122510.01
392P122510.01
401D122480.01
402L122480.01
411Y122680.02
412G122680.02
421Y122720.01
422S122720.01
431Y122620.01
432O122620.01
441Y122740.01
442K122740.01
451X122420.01
452H122420.01
461X122420.01
462T122420.01
471X122520.01
472P122520.01
481X122490.01
482L122490.01
491G123180
492S123180
501G122590.01
502O122590.01
511G122730.01
512K122730.01
521H122720
522T122720
531H122320.01
532P122320.01
541H122400.01
542L122400.01
551S122630.01
552O122630.01
561S122770.01
562K122770.01
571T122340.01
572P122340.01
581T122400.01
582L122400.01
591O122730
592K122730
601P122620
602L122620
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 396 -
Rwork0.296 7000 -
obs--99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1789-0.0517-0.20070.05310.15071.28380.0150.0386-0.0424-0.10260.0634-0.03930.1236-0.1041-0.07850.6418-0.01850.03510.7155-0.06310.3324-23.496-9.48648.712
20.13030.0530.32120.06450.18650.94980.0029-0.05810.02770.07910.0499-0.0381-0.0695-0.0942-0.05280.6558-0.0437-0.03950.7177-0.04160.3363-23.595-65.26742.926
30.5004-0.45721.08360.9472-1.64244.22380.06660.1087-0.0278-0.03940.08460.05830.04590.0684-0.15120.4926-0.1733-0.02680.6505-0.03360.4773-21.338-57.215-7.31
40.0161-0.0077-0.00690.4118-0.57920.9602-0.04990.05630.02470.03920.0708-0.0482-0.0485-0.0812-0.02090.69420.04440.17050.6028-0.08560.4207-15.70121.83954.629
50.112-0.08250.07990.2519-0.46381.1001-0.0837-0.0430.0185-0.0320.0677-0.07880.058-0.07510.0160.6815-0.086-0.18590.5972-0.07720.4351-15.981-95.87635.81
60.3712-0.11980.57460.2818-0.36641.08080.00650.0254-0.01280.06620.0136-0.16340.0729-0.0005-0.02010.6016-0.0751-0.14480.5983-0.17340.49517.207-73.60838.558
70.40670.1976-0.60080.2428-0.39861.0121-0.0109-0.05370.0207-0.07610.0163-0.144-0.06490.0354-0.00540.61230.05550.1340.5888-0.17260.48397.185-0.6252.395
80.7574-0.10340.27150.1714-0.7224.36760.0055-0.272-0.0908-0.07570.1555-0.07080.1423-0.0679-0.16090.56430.1108-0.0030.6874-0.14920.4037-1.635-7.883101.371
90.46690.3597-1.00870.8578-1.2833.53440.0225-0.11680.01450.06290.0188-0.0141-0.02730.1459-0.04130.49170.13810.01570.6816-0.04660.4575-20.909-16.94197.987
100.4335-0.0731-0.68680.3302-0.35293.51970.0897-0.10120.11910.12930.1247-0.0418-0.06240.3371-0.21440.64060.0180.14270.5973-0.14880.432-19.9923.982102.235
110.50490.14370.89070.3873-0.58283.84450.04260.1232-0.1301-0.10920.1062-0.06330.04940.2591-0.14890.6523-0.0099-0.16680.5882-0.15750.4114-19.949-78.361-11.241
120.66850.086-0.29240.096-0.47763.70340.05090.23810.04630.07850.1247-0.0188-0.2219-0.0059-0.17550.5896-0.15420.00030.6675-0.12960.4184-2.044-66.785-10.787
131.5613-0.44870.67540.2607-0.0630.5366-0.1697-0.2762-0.28510.04510.18810.09470.1491-0.0135-0.01830.5544-0.03450.05210.69610.05770.4501-62.718-18.89589.789
141.43220.01340.32730.6675-0.16050.3162-0.02020.0758-0.0306-0.21860.0347-0.02490.07840.0092-0.01450.6128-0.0085-0.03370.6545-0.00640.3501-65.547-9.79972.895
151.95720.4289-0.95150.1553-0.11940.646-0.11360.26040.3286-0.05720.18010.0992-0.15190.0195-0.06660.5504-0.0111-0.06590.68020.0580.4548-62.728-55.4071.138
161.5250.008-0.20650.6284-0.21240.292-0.0142-0.07290.01040.16280.029-0.016-0.09320.0123-0.01480.6103-0.01260.03570.6433-0.0090.3526-65.554-64.51518.021
170.362-0.7358-0.43181.93160.59811-0.1817-0.1597-0.07860.55870.1765-0.1206-0.01920.28450.00530.50490.0995-0.14950.5729-0.02290.503222.142-41.42388.86
181.8785-2.0269-1.21152.60261.07321.096-0.03930.0844-0.0813-0.26840.03770.1648-0.0148-0.20990.00160.61050.05170.08490.4241-0.22690.447919.024-42.74469.609
190.45460.85590.48332.08940.60220.983-0.13780.11650.0696-0.50540.1038-0.21120.09450.13630.0340.5091-0.12480.17230.5388-0.00180.544722.174-32.9282.034
202.66972.44651.50962.72141.08641.1303-0.0728-0.24260.2160.167-0.05680.2362-0.0147-0.30640.12970.5704-0.0803-0.10350.4557-0.24210.477519.047-31.50721.269
210.8608-0.3560.90960.1876-0.25032.24480.20350.5046-0.1922-0.1466-0.34840.0690.7397-0.49530.14490.7381-0.10920.20251.2618-0.52070.61442.223-115.327-17.364
223.3945-3.63050.15274.17920.01570.2216-0.60920.01770.00871.1320.25850.04950.27360.17160.35071.10790.27470.19820.22920.10730.743111.569-118.508-0.64
231.28141.1163-0.88631.0523-0.73990.84520.536-0.09010.14240.8016-0.22110.0867-0.3991-0.1066-0.31491.3236-0.2134-0.06450.4111-0.17180.46722.45940.236108.741
241.33971.53610.22362.71670.57590.1648-0.28550.4930.1417-0.06660.404-0.3418-0.02270.0741-0.11850.809-0.20050.00040.3610.19630.497611.2244.04991.797
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 328
2X-RAY DIFFRACTION2U9 - 328
3X-RAY DIFFRACTION3V10 - 173
4X-RAY DIFFRACTION4I9 - 325
5X-RAY DIFFRACTION5M9 - 328
6X-RAY DIFFRACTION6Q9 - 328
7X-RAY DIFFRACTION7E9 - 328
8X-RAY DIFFRACTION8F10 - 172
9X-RAY DIFFRACTION9B9 - 173
10X-RAY DIFFRACTION10J9 - 172
11X-RAY DIFFRACTION11N10 - 172
12X-RAY DIFFRACTION12R10 - 175
13X-RAY DIFFRACTION13C1 - 226
14X-RAY DIFFRACTION14D2 - 214
15X-RAY DIFFRACTION15Y1 - 226
16X-RAY DIFFRACTION16X2 - 214
17X-RAY DIFFRACTION17G1 - 226
18X-RAY DIFFRACTION18H2 - 214
19X-RAY DIFFRACTION19S1 - 226
20X-RAY DIFFRACTION20T2 - 214
21X-RAY DIFFRACTION21O1 - 226
22X-RAY DIFFRACTION22P2 - 214
23X-RAY DIFFRACTION23K1 - 226
24X-RAY DIFFRACTION24L2 - 214

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