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- PDB-4gms: Crystal structure of heterosubtypic Fab S139/1 in complex with in... -

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Basic information

Entry
Database: PDB / ID: 4gms
TitleCrystal structure of heterosubtypic Fab S139/1 in complex with influenza A H3 hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • Fab S139/1 heavy chain
  • Fab S139/1 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / immunoglobulin / virus attachment and entry / immune recognition / 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 / identical protein binding / 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
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLee, P.S. / Ekiert, D.C. / Wilson, I.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Heterosubtypic antibody recognition of the influenza virus hemagglutinin receptor binding site enhanced by avidity.
Authors: Lee, P.S. / Yoshida, R. / Ekiert, D.C. / Sakai, N. / Suzuki, Y. / Takada, A. / Wilson, I.A.
History
DepositionAug 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Jul 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 / 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_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.id / _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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
L: Fab S139/1 light chain
H: Fab S139/1 heavy chain
M: Fab S139/1 light chain
I: Fab S139/1 heavy chain
N: Fab S139/1 light chain
J: Fab S139/1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,73054
Polymers311,10712
Non-polymers11,62342
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61280 Å2
ΔGint-347 kcal/mol
Surface area111460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.510, 112.940, 196.970
Angle α, β, γ (deg.)90.00, 118.76, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 10:325 or resseq 501:501 or resseq...
21chain C and (resseq 10:325 or resseq 501:501 or resseq...
31chain E and (resseq 10:325 or resseq 501:504 or resseq...
12chain B and (resseq 1:171 or resseq 201:201 ) and (not element H)
22chain D and (resseq 1:171 or resseq 201:201 ) and (not element H)
32chain F and (resseq 1:171 or resseq 201:201 ) and (not element H)
13chain H and (resseq 1:52 or resseq 52:82 or resseq...
23chain I and (resseq 1:52 or resseq 52:82 or resseq...
33chain J and (resseq 1:52 or resseq 52:82 or resseq...
14chain L and (resseq 1:106 ) and (not element H)
24chain M and (resseq 1:106 ) and (not element H)
34chain N and (resseq 1:106 ) and (not element H)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 10:325 or resseq 501:501 or resseq...A10 - 325
121chain 'A' and (resseq 10:325 or resseq 501:501 or resseq...A501
131chain 'A' and (resseq 10:325 or resseq 501:501 or resseq...A502 - 602
141chain 'A' and (resseq 10:325 or resseq 501:501 or resseq...A504 - 701
151chain 'A' and (resseq 10:325 or resseq 501:501 or resseq...A505 - 805
161chain 'A' and (resseq 10:325 or resseq 501:501 or resseq...A510 - 902
211chain 'C' and (resseq 10:325 or resseq 501:501 or resseq...C10 - 325
221chain 'C' and (resseq 10:325 or resseq 501:501 or resseq...C501
231chain 'C' and (resseq 10:325 or resseq 501:501 or resseq...C502 - 602
241chain 'C' and (resseq 10:325 or resseq 501:501 or resseq...C504 - 701
251chain 'C' and (resseq 10:325 or resseq 501:501 or resseq...C505 - 805
261chain 'C' and (resseq 10:325 or resseq 501:501 or resseq...C510 - 903
311chain 'E' and (resseq 10:325 or resseq 501:504 or resseq...E10 - 325
321chain 'E' and (resseq 10:325 or resseq 501:504 or resseq...E501 - 504
331chain 'E' and (resseq 10:325 or resseq 501:504 or resseq...E505 - 603
341chain 'E' and (resseq 10:325 or resseq 501:504 or resseq...E508 - 702
351chain 'E' and (resseq 10:325 or resseq 501:504 or resseq...E510 - 805
361chain 'E' and (resseq 10:325 or resseq 501:504 or resseq...E515 - 904
112chain 'B' and (resseq 1:171 or resseq 201:201 ) and (not element H)B1 - 171
122chain 'B' and (resseq 1:171 or resseq 201:201 ) and (not element H)B201
212chain 'D' and (resseq 1:171 or resseq 201:201 ) and (not element H)D1 - 171
222chain 'D' and (resseq 1:171 or resseq 201:201 ) and (not element H)D201
312chain 'F' and (resseq 1:171 or resseq 201:201 ) and (not element H)F1 - 171
322chain 'F' and (resseq 1:171 or resseq 201:201 ) and (not element H)F201
113chain 'H' and (resseq 1:52 or resseq 52:82 or resseq...H1 - 52
123chain 'H' and (resseq 1:52 or resseq 52:82 or resseq...H52 - 82
133chain 'H' and (resseq 1:52 or resseq 52:82 or resseq...H82
143chain 'H' and (resseq 1:52 or resseq 52:82 or resseq...H82
153chain 'H' and (resseq 1:52 or resseq 52:82 or resseq...H82 - 100
163chain 'H' and (resseq 1:52 or resseq 52:82 or resseq...H100 - 117
213chain 'I' and (resseq 1:52 or resseq 52:82 or resseq...I1 - 52
223chain 'I' and (resseq 1:52 or resseq 52:82 or resseq...I52 - 82
233chain 'I' and (resseq 1:52 or resseq 52:82 or resseq...I82
243chain 'I' and (resseq 1:52 or resseq 52:82 or resseq...I82
253chain 'I' and (resseq 1:52 or resseq 52:82 or resseq...I82 - 100
263chain 'I' and (resseq 1:52 or resseq 52:82 or resseq...I100 - 111
273chain 'I' and (resseq 1:52 or resseq 52:82 or resseq...I116 - 117
313chain 'J' and (resseq 1:52 or resseq 52:82 or resseq...J1 - 52
323chain 'J' and (resseq 1:52 or resseq 52:82 or resseq...J52 - 82
333chain 'J' and (resseq 1:52 or resseq 52:82 or resseq...J82
343chain 'J' and (resseq 1:52 or resseq 52:82 or resseq...J82
353chain 'J' and (resseq 1:52 or resseq 52:82 or resseq...J82 - 100
363chain 'J' and (resseq 1:52 or resseq 52:82 or resseq...J100 - 117
114chain 'L' and (resseq 1:106 ) and (not element H)L0
214chain 'M' and (resseq 1:106 ) and (not element H)M0
314chain 'N' and (resseq 1:106 ) and (not element H)N0

NCS ensembles :
ID
1
2
3
4

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 35170.566 Da / Num. of mol.: 3 / Fragment: UNP residues 28-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/3/1975 H3N2 / Gene: HA / Plasmid: pFastBac / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: P03435
#2: Protein Hemagglutinin HA2 chain


Mass: 20225.393 Da / Num. of mol.: 3 / Fragment: UNP residues 347-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/3/1975 H3N2 / Gene: HA / Plasmid: pFastBac / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: P03435

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Antibody , 2 types, 6 molecules LMNHIJ

#3: Antibody Fab S139/1 light chain


Mass: 23773.053 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: S139/1 / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five
#4: Antibody Fab S139/1 heavy chain


Mass: 24533.373 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: S139/1 / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five

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Sugars , 5 types, 21 molecules

#5: 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.: 5
Source method: isolated from a genetically manipulated source
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
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#8: 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.: 2
Source method: isolated from a genetically manipulated source
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
#9: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
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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Non-polymers , 4 types, 52 molecules

#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 3.53 Å3/Da / Density % sol: 65.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 2 M ammonium sulfate, 2% v/v PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 18, 2011
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. all: 91317 / Num. obs: 91317 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 2.95→3.05 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.46 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4FNK AND 4GMT

4fnk

4gmt


Resolution: 2.95→48.406 Å / SU ML: 0.82 / σ(F): 1.34 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 4571 5.01 %RANDOM
Rwork0.2075 ---
obs0.2088 91228 99.76 %-
all-91317 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.049 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.3818 Å2-0 Å2-8.8745 Å2
2--17.4623 Å2-0 Å2
3----18.6594 Å2
Refinement stepCycle: LAST / Resolution: 2.95→48.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20687 0 742 31 21460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921956
X-RAY DIFFRACTIONf_angle_d1.17929844
X-RAY DIFFRACTIONf_dihedral_angle_d20.0888101
X-RAY DIFFRACTIONf_chiral_restr0.0683385
X-RAY DIFFRACTIONf_plane_restr0.0053748
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2577X-RAY DIFFRACTIONPOSITIONAL0.053
12C2577X-RAY DIFFRACTIONPOSITIONAL0.053
13E2577X-RAY DIFFRACTIONPOSITIONAL0.043
21B1398X-RAY DIFFRACTIONPOSITIONAL0.043
22D1398X-RAY DIFFRACTIONPOSITIONAL0.043
23F1398X-RAY DIFFRACTIONPOSITIONAL0.043
31H938X-RAY DIFFRACTIONPOSITIONAL0.464
32I938X-RAY DIFFRACTIONPOSITIONAL0.464
33J963X-RAY DIFFRACTIONPOSITIONAL0.501
41L822X-RAY DIFFRACTIONPOSITIONAL0.039
42M822X-RAY DIFFRACTIONPOSITIONAL0.039
43N822X-RAY DIFFRACTIONPOSITIONAL0.029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-2.98350.3931580.39912900X-RAY DIFFRACTION100
2.9835-3.01860.40471380.36932846X-RAY DIFFRACTION100
3.0186-3.05540.41531570.35872863X-RAY DIFFRACTION100
3.0554-3.09410.38241500.35032907X-RAY DIFFRACTION100
3.0941-3.13480.39011550.32782885X-RAY DIFFRACTION100
3.1348-3.17770.33521450.3192844X-RAY DIFFRACTION100
3.1777-3.22310.331710.31472884X-RAY DIFFRACTION100
3.2231-3.27120.32671490.29042845X-RAY DIFFRACTION100
3.2712-3.32230.28931510.27812942X-RAY DIFFRACTION100
3.3223-3.37680.28811500.26232830X-RAY DIFFRACTION100
3.3768-3.4350.30231520.2592870X-RAY DIFFRACTION100
3.435-3.49740.27611650.25762892X-RAY DIFFRACTION100
3.4974-3.56470.25911580.24192849X-RAY DIFFRACTION100
3.5647-3.63740.22821680.22452873X-RAY DIFFRACTION100
3.6374-3.71650.21141430.21692893X-RAY DIFFRACTION100
3.7165-3.80290.25211420.21722895X-RAY DIFFRACTION100
3.8029-3.8980.25211460.21562894X-RAY DIFFRACTION100
3.898-4.00330.27071500.20862881X-RAY DIFFRACTION100
4.0033-4.12110.2511430.19152871X-RAY DIFFRACTION100
4.1211-4.2540.1951760.17932856X-RAY DIFFRACTION100
4.254-4.40590.18491660.16322878X-RAY DIFFRACTION100
4.4059-4.58220.17911550.15842880X-RAY DIFFRACTION100
4.5822-4.79060.18541680.15332884X-RAY DIFFRACTION100
4.7906-5.04290.18571420.15762933X-RAY DIFFRACTION100
5.0429-5.35850.18991350.16972905X-RAY DIFFRACTION100
5.3585-5.77160.21221550.19342889X-RAY DIFFRACTION100
5.7716-6.35130.21571480.19172931X-RAY DIFFRACTION100
6.3513-7.26770.22631420.18632915X-RAY DIFFRACTION99
7.2677-9.14640.18641480.1762935X-RAY DIFFRACTION100
9.1464-48.41220.24621450.21662987X-RAY DIFFRACTION99
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)
10.30770.0736-0.32810.0180.07312.0938-0.0729-0.0845-0.0396-0.0063-0.00530.1088-0.144-0.333800.62090.10740.02670.76010.02740.837720.1965-26.73658.9016
20.4427-0.19210.10340.532-1.21820.9015-0.13360.0926-0.0007-0.0681-0.0144-0.0072-0.1905-0.4237-00.56540.082-0.1060.64-0.05540.593524.0475-23.6161-42.8694
30.3226-0.10980.10480.4564-0.85472.19040.0067-0.0118-0.2872-0.09650.05010.15770.3066-0.1279-0.1360.65110.0067-0.04740.3686-0.03350.781538.4014-53.47345.6437
40.45940.06180.2360.5539-0.07130.6289-0.05180.134-0.1525-0.23710.04310.18750.3521-0.1564-0.00850.78780.0077-0.15890.5205-0.1930.701632.1358-43.1743-44.8263
50.4045-0.04930.1371-0.0972-0.04232.44470.0115-0.074-0.0581-0.0386-0.0719-0.0613-0.14380.1016-0.00030.6722-0.01830.01820.4715-0.06450.665752.8355-24.13826.5127
60.64470.1308-0.34010.2926-0.06560.962-0.01540.2526-0.1354-0.06310.02070.04290.19080.1900.58140.0460.00950.5371-0.11990.5944.9689-26.3322-44.4963
70.3712-0.029-0.5420.53910.19810.5629-0.2307-0.0422-0.0408-0.02230.025-0.2054-0.0673-0.069400.90690.09850.02831.2848-0.04630.821212.1223-14.922750.4239
80.6076-0.96140.07360.44470.40070.18520.03850.03460.16630.341-0.23410.11640.09430.2975-00.8146-0.1475-0.07611.3181-0.04070.92195.60190.716978.8979
90.2120.0775-0.49150.8532-0.68520.7084-0.2519-0.3083-0.13540.3762-0.01830.00570.5217-0.082401.16690.0790.0691.20720.12980.735115.3444-30.71367.1989
100.18570.11310.4730.17210.48740.47610.01340.0452-0.21510.34-0.32810.14710.3081-0.0455-00.9845-0.08970.19381.4191-0.09780.8918-4.7866-6.868687.5289
110.17080.08140.28770.17880.18730.58910.2268-0.4702-0.1859-0.13710.50590.1755-0.1431-0.76690.20250.8023-0.08610.00680.99850.57441.179733.2455-73.025443.9388
12-0.078-0.1018-0.00990.04080.2072-0.0131-0.1436-0.2393-0.1937-0.05990.7780.5753-0.5347-0.0281-01.6864-0.11920.20241.72320.94431.651229.9364-99.69365.8544
130.06330.14190.54560.5594-0.35520.2445-0.2986-0.5703-0.09860.23570.4278-0.0169-0.1199-0.22370.00010.81170.22180.25421.20910.25270.753445.2951-66.953862.2745
14-0.034-0.0989-0.07080.18910.12760.00690.9629-0.417-1.09851.24940.9984-0.06170.34780.16140.02491.9530.2135-0.03141.4380.48771.563243.0296-94.842471.0406
150.70260.20420.41590.2008-0.2260.26620.3381-0.6563-0.19480.0898-0.31870.087-0.03980.197800.9333-0.1708-0.11941.45-0.07520.702874.0265-24.769345.3175
160.04120.4350.10580.08230.0025-0.1137-0.51480.67560.1360.19680.4976-0.28820.07580.4326-01.4608-0.1583-0.28582.1002-0.01311.025699.4724-22.26270.1083
170.14370.01290.29630.12840.20510.3354-0.0785-0.87610.25480.1264-0.2050.0283-0.1044-0.132401.0665-0.0484-0.02831.8135-0.03260.707262.4537-21.576364.8042
180.0448-0.0967-0.00730.10850.22010.2518-0.35880.24410.57650.05890.4331-0.01120.4278-0.431-01.475-0.1296-0.30661.86220.17371.063594.6147-8.333877.2972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA10 - 325
2X-RAY DIFFRACTION2chain BB1 - 171
3X-RAY DIFFRACTION3chain CC10 - 325
4X-RAY DIFFRACTION4chain DD1 - 171
5X-RAY DIFFRACTION5chain EE10 - 325
6X-RAY DIFFRACTION6chain FF1 - 171
7X-RAY DIFFRACTION7chain H and resid 1:118 or chain H and resid 301:302H1 - 118
8X-RAY DIFFRACTION7chain H and resid 1:118 or chain H and resid 301:302H301 - 302
9X-RAY DIFFRACTION8chain H and resid 119:213H119 - 213
10X-RAY DIFFRACTION9chain L and resid 1:109L1 - 109
11X-RAY DIFFRACTION10chain L and resid 110:211L110 - 211
12X-RAY DIFFRACTION11chain I and resid 1:118 or chain I and resid 301:301I1 - 118
13X-RAY DIFFRACTION11chain I and resid 1:118 or chain I and resid 301:301I301
14X-RAY DIFFRACTION12chain I and resid 119:205I119 - 205
15X-RAY DIFFRACTION13chain M and resid 1:109M1 - 109
16X-RAY DIFFRACTION14chain M and resid 110:180M110 - 180
17X-RAY DIFFRACTION15chain J and resid 1:118 or chain J and resid 301:301J1 - 118
18X-RAY DIFFRACTION15chain J and resid 1:118 or chain J and resid 301:301J301
19X-RAY DIFFRACTION16chain J and resid 119:213J119 - 213
20X-RAY DIFFRACTION17chain N and resid 1:109N1 - 109
21X-RAY DIFFRACTION18chain N and resid 110:213N110 - 213

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