PDB-5o87: Crystal structure of wild type Aplysia californica AChBP in compl...

ID or keywords:

Entry

Database: PDB / ID: 5o87

Title

Crystal structure of wild type Aplysia californica AChBP in complex with nicotine

Components

Soluble acetylcholine receptor

Keywords

SIGNALING PROTEIN / receptor

Function / homology

Function and homology information

extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
Similarity search - Function

Biological species

Aplysia californica (California sea hare)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Dawson, A. / Hunter, W.N. / de Souza, J.O. / Trumper, P.

Funding support

United Kingdom, 1items

Citation

Journal: Iucrj / Year: 2019
Title: Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein.
Authors: Dawson, A. / Trumper, P. / de Souza, J.O. / Parker, H. / Jones, M.J. / Hales, T.G. / Hunter, W.N.

History

Deposition	Jun 12, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 27, 2018	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2020	Group: Data collection / Database references / Category: chem_comp / citation / citation_author Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Jan 17, 2024	Group: 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 / pdbx_initial_refinement_model / 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
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5o87.cif.gz	470.3 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o8/5o87 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/5o87	HTTPS FTP

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Related structure data

Related structure data	5o8tC 5oa0C 5oadC 5oajC 5oalC 5oanC 5obgC 2xysS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6qqo-1 5obg-d 6sgv-1 6sh0-1 5oan-d 5oa0-d 6qkk-1 4bqt-d 2br7-d 6sh0-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (4) #71 - Nov 2005 Acetylcholine Receptor similarity (4) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

292 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Soluble acetylcholine receptor

B: Soluble acetylcholine receptor

C: Soluble acetylcholine receptor

D: Soluble acetylcholine receptor

E: Soluble acetylcholine receptor

hetero molecules

defined by software
146 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Soluble acetylcholine receptor

G: Soluble acetylcholine receptor

H: Soluble acetylcholine receptor

I: Soluble acetylcholine receptor

J: Soluble acetylcholine receptor

hetero molecules

defined by software
146 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	210.781, 131.999, 130.655
Angle α, β, γ (deg.)	90.00, 103.15, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	A	A	20 - 224	20 - 224
2	1	ARG	ARG	B	B	20 - 224	20 - 224
1	2	ARG	ARG	A	A	20 - 225	20 - 225
2	2	ARG	ARG	C	C	20 - 225	20 - 225
1	3	ARG	ARG	A	A	20 - 225	20 - 225
2	3	ARG	ARG	D	D	20 - 225	20 - 225
1	4	ARG	ARG	A	A	20 - 225	20 - 225
2	4	ARG	ARG	E	E	20 - 225	20 - 225
1	5	ARG	ARG	A	A	20 - 225	20 - 225
2	5	ARG	ARG	F	F	20 - 225	20 - 225
1	6	ARG	ARG	A	A	20 - 225	20 - 225
2	6	ARG	ARG	G	G	20 - 225	20 - 225
1	7	GLU	GLU	A	A	20 - 223	20 - 223
2	7	GLU	GLU	H	H	20 - 223	20 - 223
1	8	ARG	ARG	A	A	20 - 225	20 - 225
2	8	ARG	ARG	I	I	20 - 225	20 - 225
1	9	ARG	ARG	A	A	20 - 225	20 - 225
2	9	ARG	ARG	J	J	20 - 225	20 - 225
1	10	ARG	ARG	B	B	20 - 224	20 - 224
2	10	ARG	ARG	C	C	20 - 224	20 - 224
1	11	ARG	ARG	B	B	20 - 224	20 - 224
2	11	ARG	ARG	D	D	20 - 224	20 - 224
1	12	ARG	ARG	B	B	20 - 224	20 - 224
2	12	ARG	ARG	E	E	20 - 224	20 - 224
1	13	ARG	ARG	B	B	20 - 224	20 - 224
2	13	ARG	ARG	F	F	20 - 224	20 - 224
1	14	ARG	ARG	B	B	20 - 224	20 - 224
2	14	ARG	ARG	G	G	20 - 224	20 - 224
1	15	GLU	GLU	B	B	20 - 223	20 - 223
2	15	GLU	GLU	H	H	20 - 223	20 - 223
1	16	ARG	ARG	B	B	20 - 224	20 - 224
2	16	ARG	ARG	I	I	20 - 224	20 - 224
1	17	ARG	ARG	B	B	20 - 224	20 - 224
2	17	ARG	ARG	J	J	20 - 224	20 - 224
1	18	ARG	ARG	C	C	20 - 225	20 - 225
2	18	ARG	ARG	D	D	20 - 225	20 - 225
1	19	ARG	ARG	C	C	20 - 225	20 - 225
2	19	ARG	ARG	E	E	20 - 225	20 - 225
1	20	ARG	ARG	C	C	20 - 225	20 - 225
2	20	ARG	ARG	F	F	20 - 225	20 - 225
1	21	ARG	ARG	C	C	20 - 225	20 - 225
2	21	ARG	ARG	G	G	20 - 225	20 - 225
1	22	GLU	GLU	C	C	20 - 223	20 - 223
2	22	GLU	GLU	H	H	20 - 223	20 - 223
1	23	ARG	ARG	C	C	20 - 225	20 - 225
2	23	ARG	ARG	I	I	20 - 225	20 - 225
1	24	ARG	ARG	C	C	20 - 225	20 - 225
2	24	ARG	ARG	J	J	20 - 225	20 - 225
1	25	ARG	ARG	D	D	20 - 225	20 - 225
2	25	ARG	ARG	E	E	20 - 225	20 - 225
1	26	ARG	ARG	D	D	20 - 225	20 - 225
2	26	ARG	ARG	F	F	20 - 225	20 - 225
1	27	ARG	ARG	D	D	20 - 225	20 - 225
2	27	ARG	ARG	G	G	20 - 225	20 - 225
1	28	GLU	GLU	D	D	20 - 223	20 - 223
2	28	GLU	GLU	H	H	20 - 223	20 - 223
1	29	ARG	ARG	D	D	20 - 225	20 - 225
2	29	ARG	ARG	I	I	20 - 225	20 - 225
1	30	ARG	ARG	D	D	20 - 225	20 - 225
2	30	ARG	ARG	J	J	20 - 225	20 - 225
1	31	ARG	ARG	E	E	20 - 225	20 - 225
2	31	ARG	ARG	F	F	20 - 225	20 - 225
1	32	ARG	ARG	E	E	20 - 225	20 - 225
2	32	ARG	ARG	G	G	20 - 225	20 - 225
1	33	GLU	GLU	E	E	20 - 223	20 - 223
2	33	GLU	GLU	H	H	20 - 223	20 - 223
1	34	ARG	ARG	E	E	20 - 225	20 - 225
2	34	ARG	ARG	I	I	20 - 225	20 - 225
1	35	ARG	ARG	E	E	20 - 225	20 - 225
2	35	ARG	ARG	J	J	20 - 225	20 - 225
1	36	ARG	ARG	F	F	20 - 225	20 - 225
2	36	ARG	ARG	G	G	20 - 225	20 - 225
1	37	GLU	GLU	F	F	20 - 223	20 - 223
2	37	GLU	GLU	H	H	20 - 223	20 - 223
1	38	ARG	ARG	F	F	20 - 225	20 - 225
2	38	ARG	ARG	I	I	20 - 225	20 - 225
1	39	ARG	ARG	F	F	20 - 225	20 - 225
2	39	ARG	ARG	J	J	20 - 225	20 - 225
1	40	GLU	GLU	G	G	20 - 223	20 - 223
2	40	GLU	GLU	H	H	20 - 223	20 - 223
1	41	ARG	ARG	G	G	20 - 225	20 - 225
2	41	ARG	ARG	I	I	20 - 225	20 - 225
1	42	ARG	ARG	G	G	20 - 225	20 - 225
2	42	ARG	ARG	J	J	20 - 225	20 - 225
1	43	GLU	GLU	H	H	20 - 223	20 - 223
2	43	GLU	GLU	I	I	20 - 223	20 - 223
1	44	GLU	GLU	H	H	20 - 223	20 - 223
2	44	GLU	GLU	J	J	20 - 223	20 - 223
1	45	ARG	ARG	I	I	20 - 225	20 - 225
2	45	ARG	ARG	J	J	20 - 225	20 - 225

NCS ensembles :

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

#1: Protein

Soluble acetylcholine receptor

Mass: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aplysia californica (California sea hare)
Production host:

Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8

#3: 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.: 10
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 5 types, 1883 molecules

#2: Chemical	ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE Mass: 162.232 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C₁₀H₁₄N₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O / Comment: alkaloid*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1801 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.59 % / Description: block
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.45 M ammonium phosphate monobasic 2 % glycerol 2 % IPA

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Data collection

Diffraction	Mean temperature: 150 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54157 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 8, 2016 / Details: Varimax Cu-VHF
Radiation	Monochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54157 Å / Relative weight: 1
Reflection	Resolution: 2.2→25.2 Å / Num. obs: 176070 / % possible obs: 99.9 % / Redundancy: 6.8 % / B_iso Wilson estimate: 27.2 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.115 / Net I/σ(I): 8.8
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.639 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 8731 / CC_1/2: 0.675 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2xys

2xys

Resolution: 2.2→25.2 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.936 / SU B: 5.302 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23515	8653	4.9 %	RANDOM
R_work	0.20286	-	-	-
obs	0.20444	167118	99.71 %	-

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 34.896 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.93 Å²	0 Å²	-0.24 Å²
2-	-	1.53 Å²	0 Å²
3-	-	-	0.46 Å²

Refinement step

Cycle: 1 / Resolution: 2.2→25.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16502	0	568	1801	18871

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	17469
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.02	15600
X-RAY DIFFRACTION	r_angle_refined_deg	1.451	1.979	23763
X-RAY DIFFRACTION	r_angle_other_deg	0.972	3.001	36263
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.205	5.017	2057
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.957	24.396	803
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.99	15	2762
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.259	15	99
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2665
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	19006
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3516
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	5.902	3.039	8250
X-RAY DIFFRACTION	r_mcbond_other	5.902	3.038	8249
X-RAY DIFFRACTION	r_mcangle_it	6.849	4.529	10295
X-RAY DIFFRACTION	r_mcangle_other	6.849	4.531	10296
X-RAY DIFFRACTION	r_scbond_it	9.273	3.846	9219
X-RAY DIFFRACTION	r_scbond_other	9.272	3.846	9220
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	12.036	5.496	13469
X-RAY DIFFRACTION	r_long_range_B_refined	12.976	38.507	19360
X-RAY DIFFRACTION	r_long_range_B_other	13.003	37.983	18945
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

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

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	13198	0.04
1	2	B	13198	0.04
2	1	A	13390	0.04
2	2	C	13390	0.04
3	1	A	13320	0.05
3	2	D	13320	0.05
4	1	A	13362	0.04
4	2	E	13362	0.04
5	1	A	13320	0.04
5	2	F	13320	0.04
6	1	A	13336	0.05
6	2	G	13336	0.05
7	1	A	13214	0.04
7	2	H	13214	0.04
8	1	A	13324	0.05
8	2	I	13324	0.05
9	1	A	13316	0.04
9	2	J	13316	0.04
10	1	B	13278	0.03
10	2	C	13278	0.03
11	1	B	13240	0.04
11	2	D	13240	0.04
12	1	B	13278	0.04
12	2	E	13278	0.04
13	1	B	13290	0.04
13	2	F	13290	0.04
14	1	B	13232	0.04
14	2	G	13232	0.04
15	1	B	13232	0.04
15	2	H	13232	0.04
16	1	B	13262	0.04
16	2	I	13262	0.04
17	1	B	13284	0.04
17	2	J	13284	0.04
18	1	C	13392	0.04
18	2	D	13392	0.04
19	1	C	13444	0.02
19	2	E	13444	0.02
20	1	C	13432	0.03
20	2	F	13432	0.03
21	1	C	13434	0.04
21	2	G	13434	0.04
22	1	C	13270	0.03
22	2	H	13270	0.03
23	1	C	13428	0.03
23	2	I	13428	0.03
24	1	C	13414	0.03
24	2	J	13414	0.03
25	1	D	13400	0.04
25	2	E	13400	0.04
26	1	D	13356	0.05
26	2	F	13356	0.05
27	1	D	13488	0.04
27	2	G	13488	0.04
28	1	D	13276	0.05
28	2	H	13276	0.05
29	1	D	13454	0.04
29	2	I	13454	0.04
30	1	D	13356	0.05
30	2	J	13356	0.05
31	1	E	13458	0.02
31	2	F	13458	0.02
32	1	E	13354	0.04
32	2	G	13354	0.04
33	1	E	13266	0.03
33	2	H	13266	0.03
34	1	E	13414	0.04
34	2	I	13414	0.04
35	1	E	13458	0.02
35	2	J	13458	0.02
36	1	F	13350	0.04
36	2	G	13350	0.04
37	1	F	13232	0.04
37	2	H	13232	0.04
38	1	F	13410	0.04
38	2	I	13410	0.04
39	1	F	13484	0.03
39	2	J	13484	0.03
40	1	G	13238	0.03
40	2	H	13238	0.03
41	1	G	13456	0.03
41	2	I	13456	0.03
42	1	G	13342	0.05
42	2	J	13342	0.05
43	1	H	13264	0.04
43	2	I	13264	0.04
44	1	H	13224	0.04
44	2	J	13224	0.04
45	1	I	13440	0.04
45	2	J	13440	0.04

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.316	641	-
R_work	0.273	12260	-
obs	-	-	99.7 %

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

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Non-polymers , 5 types, 1883 molecules

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

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Non-polymers , 5 types, 1883 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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