PDB-6hkv: Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in ...

ID or keywords:

Entry

Database: PDB / ID: 6hkv

Title

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers

Components

Capsid protein VP1

Keywords

VIRAL PROTEIN / SIALIC ACID DERIVATIVE

Function / homology

Function and homology information

T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function

Biological species

Trichodysplasia spinulosa-associated polyomavirus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Rustmeier, N.H. / Stehle, T.

Funding support

Germany, 1items

Citation

Journal: Macromol Biosci / Year: 2019
Title: Divalent Sialylated Precision Glycooligomers Binding to Polyomaviruses and the Effect of Different Linkers.
Authors: Baier, M. / Rustmeier, N.H. / Harr, J. / Cyrus, N. / Reiss, G.J. / Grafmuller, A. / Blaum, B.S. / Stehle, T. / Hartmann, L.

History

Deposition	Sep 8, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 27, 2019	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2019	Group: Data collection / Database references Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.journal_volume
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6hkv.cif.gz	602.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6hkv.ent.gz	476.9 KB	Display	PDB format
PDBx/mmJSON format	6hkv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hk/6hkv ftp://data.pdbj.org/pub/pdb/validation_reports/hk/6hkv	HTTPS FTP

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Related structure data

Related structure data	6hkuC 4u60S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4u61-1 4fmg-3 4fmi-1 5cpx-d 6y5z-d 4fmi-3 4fmj-3 4x16-d 4jce-d 4fmg-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	#47 - Nov 2003 Simian Virus 40 similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (5)

Deposited unit

A: Capsid protein VP1

B: Capsid protein VP1

C: Capsid protein VP1

D: Capsid protein VP1

E: Capsid protein VP1

F: Capsid protein VP1

G: Capsid protein VP1

H: Capsid protein VP1

I: Capsid protein VP1

J: Capsid protein VP1

hetero molecules

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

1

A: Capsid protein VP1

B: Capsid protein VP1

C: Capsid protein VP1

D: Capsid protein VP1

E: Capsid protein VP1

hetero molecules

defined by author&software
Evidence: gel filtration
162 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Capsid protein VP1

G: Capsid protein VP1

H: Capsid protein VP1

I: Capsid protein VP1

J: Capsid protein VP1

hetero molecules

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

Unit cell

Length a, b, c (Å)	138.400, 145.705, 149.453
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	ARG	ARG	A	A	32 - 302	1 - 271
2	1	ASN	ASN	ARG	ARG	B	B	32 - 302	1 - 271
1	2	ASN	ASN	ASN	ASN	A	A	32 - 303	1 - 272
2	2	ASN	ASN	ASN	ASN	C	C	32 - 303	1 - 272
1	3	ASN	ASN	ARG	ARG	A	A	32 - 302	1 - 271
2	3	ASN	ASN	ARG	ARG	D	D	32 - 302	1 - 271
1	4	ILE	ILE	ASN	ASN	A	A	33 - 303	2 - 272
2	4	ILE	ILE	ASN	ASN	E	E	33 - 303	2 - 272
1	5	ASN	ASN	ASN	ASN	A	A	32 - 303	1 - 272
2	5	ASN	ASN	ASN	ASN	F	F	32 - 303	1 - 272
1	6	ILE	ILE	ASN	ASN	A	A	33 - 303	2 - 272
2	6	ILE	ILE	ASN	ASN	G	G	33 - 303	2 - 272
1	7	ILE	ILE	ASN	ASN	A	A	33 - 303	2 - 272
2	7	ILE	ILE	ASN	ASN	H	H	33 - 303	2 - 272
1	8	ASN	ASN	ASN	ASN	A	A	32 - 303	1 - 272
2	8	ASN	ASN	ASN	ASN	I	I	32 - 303	1 - 272
1	9	ASN	ASN	ARG	ARG	A	A	32 - 302	1 - 271
2	9	ASN	ASN	ARG	ARG	J	J	32 - 302	1 - 271
1	10	ASN	ASN	ARG	ARG	B	B	32 - 302	1 - 271
2	10	ASN	ASN	ARG	ARG	C	C	32 - 302	1 - 271
1	11	ASN	ASN	ARG	ARG	B	B	32 - 302	1 - 271
2	11	ASN	ASN	ARG	ARG	D	D	32 - 302	1 - 271
1	12	ILE	ILE	VAL	VAL	B	B	33 - 301	2 - 270
2	12	ILE	ILE	VAL	VAL	E	E	33 - 301	2 - 270
1	13	ASN	ASN	ARG	ARG	B	B	32 - 302	1 - 271
2	13	ASN	ASN	ARG	ARG	F	F	32 - 302	1 - 271
1	14	ILE	ILE	ARG	ARG	B	B	33 - 302	2 - 271
2	14	ILE	ILE	ARG	ARG	G	G	33 - 302	2 - 271
1	15	ILE	ILE	VAL	VAL	B	B	33 - 301	2 - 270
2	15	ILE	ILE	VAL	VAL	H	H	33 - 301	2 - 270
1	16	ASN	ASN	ARG	ARG	B	B	32 - 302	1 - 271
2	16	ASN	ASN	ARG	ARG	I	I	32 - 302	1 - 271
1	17	ASN	ASN	ARG	ARG	B	B	32 - 302	1 - 271
2	17	ASN	ASN	ARG	ARG	J	J	32 - 302	1 - 271
1	18	ASN	ASN	ARG	ARG	C	C	32 - 302	1 - 271
2	18	ASN	ASN	ARG	ARG	D	D	32 - 302	1 - 271
1	19	ILE	ILE	ASN	ASN	C	C	33 - 303	2 - 272
2	19	ILE	ILE	ASN	ASN	E	E	33 - 303	2 - 272
1	20	ASN	ASN	ASN	ASN	C	C	32 - 303	1 - 272
2	20	ASN	ASN	ASN	ASN	F	F	32 - 303	1 - 272
1	21	ILE	ILE	ARG	ARG	C	C	33 - 302	2 - 271
2	21	ILE	ILE	ARG	ARG	G	G	33 - 302	2 - 271
1	22	ILE	ILE	ASN	ASN	C	C	33 - 303	2 - 272
2	22	ILE	ILE	ASN	ASN	H	H	33 - 303	2 - 272
1	23	ASN	ASN	ASN	ASN	C	C	32 - 303	1 - 272
2	23	ASN	ASN	ASN	ASN	I	I	32 - 303	1 - 272
1	24	ASN	ASN	ARG	ARG	C	C	32 - 302	1 - 271
2	24	ASN	ASN	ARG	ARG	J	J	32 - 302	1 - 271
1	25	ILE	ILE	ARG	ARG	D	D	33 - 302	2 - 271
2	25	ILE	ILE	ARG	ARG	E	E	33 - 302	2 - 271
1	26	ASN	ASN	ARG	ARG	D	D	32 - 302	1 - 271
2	26	ASN	ASN	ARG	ARG	F	F	32 - 302	1 - 271
1	27	ILE	ILE	ARG	ARG	D	D	33 - 302	2 - 271
2	27	ILE	ILE	ARG	ARG	G	G	33 - 302	2 - 271
1	28	ILE	ILE	VAL	VAL	D	D	33 - 301	2 - 270
2	28	ILE	ILE	VAL	VAL	H	H	33 - 301	2 - 270
1	29	ASN	ASN	ARG	ARG	D	D	32 - 302	1 - 271
2	29	ASN	ASN	ARG	ARG	I	I	32 - 302	1 - 271
1	30	ASN	ASN	ARG	ARG	D	D	32 - 302	1 - 271
2	30	ASN	ASN	ARG	ARG	J	J	32 - 302	1 - 271
1	31	ILE	ILE	ASN	ASN	E	E	33 - 303	2 - 272
2	31	ILE	ILE	ASN	ASN	F	F	33 - 303	2 - 272
1	32	ILE	ILE	ASN	ASN	E	E	33 - 303	2 - 272
2	32	ILE	ILE	ASN	ASN	G	G	33 - 303	2 - 272
1	33	ILE	ILE	ASN	ASN	E	E	33 - 303	2 - 272
2	33	ILE	ILE	ASN	ASN	H	H	33 - 303	2 - 272
1	34	ILE	ILE	ASN	ASN	E	E	33 - 303	2 - 272
2	34	ILE	ILE	ASN	ASN	I	I	33 - 303	2 - 272
1	35	ILE	ILE	VAL	VAL	E	E	33 - 301	2 - 270
2	35	ILE	ILE	VAL	VAL	J	J	33 - 301	2 - 270
1	36	ILE	ILE	ARG	ARG	F	F	33 - 302	2 - 271
2	36	ILE	ILE	ARG	ARG	G	G	33 - 302	2 - 271
1	37	ILE	ILE	ASN	ASN	F	F	33 - 303	2 - 272
2	37	ILE	ILE	ASN	ASN	H	H	33 - 303	2 - 272
1	38	ASN	ASN	ASN	ASN	F	F	32 - 303	1 - 272
2	38	ASN	ASN	ASN	ASN	I	I	32 - 303	1 - 272
1	39	ASN	ASN	ARG	ARG	F	F	32 - 302	1 - 271
2	39	ASN	ASN	ARG	ARG	J	J	32 - 302	1 - 271
1	40	ILE	ILE	ASN	ASN	G	G	33 - 303	2 - 272
2	40	ILE	ILE	ASN	ASN	H	H	33 - 303	2 - 272
1	41	ILE	ILE	ASN	ASN	G	G	33 - 303	2 - 272
2	41	ILE	ILE	ASN	ASN	I	I	33 - 303	2 - 272
1	42	ILE	ILE	ARG	ARG	G	G	33 - 302	2 - 271
2	42	ILE	ILE	ARG	ARG	J	J	33 - 302	2 - 271
1	43	ILE	ILE	ASN	ASN	H	H	33 - 303	2 - 272
2	43	ILE	ILE	ASN	ASN	I	I	33 - 303	2 - 272
1	44	ILE	ILE	VAL	VAL	H	H	33 - 301	2 - 270
2	44	ILE	ILE	VAL	VAL	J	J	33 - 301	2 - 270
1	45	ASN	ASN	ARG	ARG	I	I	32 - 302	1 - 271
2	45	ASN	ASN	ARG	ARG	J	J	32 - 302	1 - 271

NCS ensembles :

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein	Capsid protein VP1 / Mass: 30220.982 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichodysplasia spinulosa-associated polyomavirus Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E2ESL7

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Non-polymers , 5 types, 2867 molecules

#2: Chemical	ChemComp-GXB / Sialylated precision glycomacromolecule Mass: 2135.192 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₉₂H₁₃₉N₁₉O₃₉ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2853 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.47 Å³/Da / Density % sol: 50.19 % / Description: three dimensional, cubic or rectangular blocks
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium malonate pH 5.0

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 27, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→47.95 Å / Num. obs: 302337 / % possible obs: 99.97 % / Redundancy: 8.7 % / B_iso Wilson estimate: 26.26 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.11 / Net I/σ(I): 15.72
Reflection shell	Resolution: 1.75→1.81 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 29947 / CC_1/2: 0.48 / R_rim(I) all: 1.78 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0230	refinement
XDS		data reduction
PDB_EXTRACT	3.24	data extraction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4u60

4u60

Resolution: 1.75→47.95 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.958 / SU B: 2.638 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.1
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.201	3027	1 %	RANDOM
R_work	0.1759	-	-	-
obs	0.1761	299628	99.82 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 104.3 Å² / B_iso mean: 28.649 Å² / B_iso min: 16.01 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	-0 Å²	-0 Å²
2-	-	-0.68 Å²	0 Å²
3-	-	-	0.4 Å²

Refinement step

Cycle: final / Resolution: 1.75→47.95 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20567	0	285	2873	23725
B_iso mean	-	-	42.44	37.7	-
Num. residues	-	-	-	-	2680

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.014	21549
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	18764
X-RAY DIFFRACTION	r_angle_refined_deg	1.302	1.683	29413
X-RAY DIFFRACTION	r_angle_other_deg	0.938	1.647	44066
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.859	5	2728
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.369	23.587	1012
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.864	15	3421
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.185	15	92
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	2862
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	24325
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3841

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	8279	0.06
1	2	B	8279	0.06
2	1	A	8477	0.08
2	2	C	8477	0.08
3	1	A	8272	0.07
3	2	D	8272	0.07
4	1	A	8244	0.07
4	2	E	8244	0.07
5	1	A	8536	0.07
5	2	F	8536	0.07
6	1	A	8427	0.08
6	2	G	8427	0.08
7	1	A	8315	0.06
7	2	H	8315	0.06
8	1	A	8363	0.07
8	2	I	8363	0.07
9	1	A	8329	0.06
9	2	J	8329	0.06
10	1	B	8230	0.06
10	2	C	8230	0.06
11	1	B	8307	0.06
11	2	D	8307	0.06
12	1	B	8187	0.06
12	2	E	8187	0.06
13	1	B	8278	0.06
13	2	F	8278	0.06
14	1	B	8169	0.06
14	2	G	8169	0.06
15	1	B	8270	0.06
15	2	H	8270	0.06
16	1	B	8267	0.06
16	2	I	8267	0.06
17	1	B	8311	0.05
17	2	J	8311	0.05
18	1	C	8297	0.06
18	2	D	8297	0.06
19	1	C	8355	0.07
19	2	E	8355	0.07
20	1	C	8527	0.08
20	2	F	8527	0.08
21	1	C	8401	0.08
21	2	G	8401	0.08
22	1	C	8361	0.06
22	2	H	8361	0.06
23	1	C	8428	0.07
23	2	I	8428	0.07
24	1	C	8327	0.06
24	2	J	8327	0.06
25	1	D	8256	0.06
25	2	E	8256	0.06
26	1	D	8278	0.07
26	2	F	8278	0.07
27	1	D	8192	0.07
27	2	G	8192	0.07
28	1	D	8289	0.06
28	2	H	8289	0.06
29	1	D	8287	0.07
29	2	I	8287	0.07
30	1	D	8340	0.05
30	2	J	8340	0.05
31	1	E	8366	0.07
31	2	F	8366	0.07
32	1	E	8246	0.08
32	2	G	8246	0.08
33	1	E	8331	0.06
33	2	H	8331	0.06
34	1	E	8364	0.07
34	2	I	8364	0.07
35	1	E	8293	0.05
35	2	J	8293	0.05
36	1	F	8394	0.08
36	2	G	8394	0.08
37	1	F	8358	0.06
37	2	H	8358	0.06
38	1	F	8445	0.06
38	2	I	8445	0.06
39	1	F	8358	0.06
39	2	J	8358	0.06
40	1	G	8260	0.07
40	2	H	8260	0.07
41	1	G	8407	0.08
41	2	I	8407	0.08
42	1	G	8258	0.07
42	2	J	8258	0.07
43	1	H	8303	0.06
43	2	I	8303	0.06
44	1	H	8290	0.05
44	2	J	8290	0.05
45	1	I	8243	0.06
45	2	J	8243	0.06

LS refinement shell

Resolution: 1.748→1.794 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.353	218	-
R_work	0.32	21552	-
all	-	21770	-
obs	-	-	97.83 %

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Protein , 1 types, 10 molecules ABCDEFGHIJ

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Non-polymers , 5 types, 2867 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi