PDB-5hzn: Structure of NVP-AEW541 in complex with IGF-1R kinase

ID or keywords:

Entry

Database: PDB / ID: 5hzn

Title

Structure of NVP-AEW541 in complex with IGF-1R kinase

Components

Insulin-like growth factor 1 receptor

Keywords

TRANSFERASE / Inhibitor / Kinase

Function / homology

Function and homology information

protein kinase complex / insulin-like growth factor receptor activity / insulin-like growth factor binding / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / protein transporter activity / IRS-related events triggered by IGF1R / transcytosis / insulin receptor complex / insulin-like growth factor I binding / positive regulation of protein-containing complex disassembly ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Cowan-Jacob, S.W.

Citation

Journal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Identification of a 5-[3-phenyl-(2-cyclic-ether)-methylether]-4-aminopyrrolo[2,3-d]pyrimidine series of IGF-1R inhibitors.
Authors: Stauffer, F. / Cowan-Jacob, S.W. / Scheufler, C. / Furet, P.

History

Deposition	Feb 2, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Apr 6, 2016	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2016	Group: Refinement description
Revision 1.2	May 8, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hzn.cif.gz	484.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5hzn.ent.gz	400.8 KB	Display	PDB format
PDBx/mmJSON format	5hzn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hzn_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	5hzn_full_validation.pdf.gz	2.6 MB	Display
Data in XML	5hzn_validation.xml.gz	92.1 KB	Display
Data in CIF	5hzn_validation.cif.gz	122.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hz/5hzn ftp://data.pdbj.org/pub/pdb/validation_reports/hz/5hzn	HTTPS FTP

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Related structure data

Related structure data	5hhwC C: citing same article (ref.)
Similar structure data	4y5f-d 7age-1 7agc-3 1u5r-1 3fv3-1 4y3i-d 2r6h-1 3fqg-d 4j96-1 1ewy-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5hhwC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#182 - Feb 2015 Insulin receptor similarity (11) #126 - Jun 2010 Epidermal Growth Factor similarity (8) #52 - Apr 2004 Growth Hormone similarity (3) #68 - Aug 2005 Neurotrophins similarity (2) #148 - Apr 2012 Ras Protein similarity (1) #184 - Apr 2015 Glucagon similarity (3) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Insulin-like growth factor 1 receptor

B: Insulin-like growth factor 1 receptor

C: Insulin-like growth factor 1 receptor

D: Insulin-like growth factor 1 receptor

E: Insulin-like growth factor 1 receptor

F: Insulin-like growth factor 1 receptor

G: Insulin-like growth factor 1 receptor

H: Insulin-like growth factor 1 receptor

hetero molecules

282 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

E: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

F: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

G: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

H: Insulin-like growth factor 1 receptor

hetero molecules

defined by author
35.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.435, 190.045, 155.488
Angle α, β, γ (deg.)	90.000, 90.220, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	CYS	CYS	1	A	A	980 - 1056	1 - 77
2	1	1	ALA	ALA	CYS	CYS	1	E	E	980 - 1056	1 - 77
1	2	1	ARG	ARG	GLY	GLY	1	A	A	1131 - 1149	152 - 170
2	2	1	ARG	ARG	GLY	GLY	1	E	E	1131 - 1149	152 - 170
1	3	1	PHE	PHE	LYS	LYS	1	A	A	1151 - 1283	172 - 304
2	3	1	PHE	PHE	LYS	LYS	1	E	E	1151 - 1283	172 - 304
1	4	1	HIS	HIS	VAL	VAL	1	A	A	1058 - 1129	79 - 150
2	4	1	HIS	HIS	VAL	VAL	1	E	E	1058 - 1129	79 - 150
1	1	2	ALA	ALA	CYS	CYS	1	B	B	980 - 1056	1 - 77
2	1	2	ALA	ALA	CYS	CYS	1	F	F	980 - 1056	1 - 77
1	2	2	ARG	ARG	GLY	GLY	1	B	B	1131 - 1149	152 - 170
2	2	2	ARG	ARG	GLY	GLY	1	F	F	1131 - 1149	152 - 170
1	3	2	PHE	PHE	LYS	LYS	1	B	B	1151 - 1283	172 - 304
2	3	2	PHE	PHE	LYS	LYS	1	F	F	1151 - 1283	172 - 304
1	4	2	HIS	HIS	VAL	VAL	1	B	B	1058 - 1129	79 - 150
2	4	2	HIS	HIS	VAL	VAL	1	F	F	1058 - 1129	79 - 150
1	1	3	ALA	ALA	LYS	LYS	1	C	C	980 - 1283	1 - 304
2	1	3	ALA	ALA	LYS	LYS	1	G	G	980 - 1283	1 - 304
1	1	4	ALA	ALA	CYS	CYS	1	D	D	980 - 1056	1 - 77
2	1	4	ALA	ALA	CYS	CYS	1	H	H	980 - 1056	1 - 77
1	2	4	HIS	HIS	GLY	GLY	1	D	D	1058 - 1149	79 - 170
2	2	4	HIS	HIS	GLY	GLY	1	H	H	1058 - 1149	79 - 170
1	3	4	PHE	PHE	ASN	ASN	1	D	D	1151 - 1282	172 - 303
2	3	4	PHE	PHE	ASN	ASN	1	H	H	1151 - 1282	172 - 303
1	1	5	ASP	ASP	GLY	GLY	4	A	A	982 - 1003	3 - 24
2	1	5	ASP	ASP	GLY	GLY	4	B	B	982 - 1003	3 - 24
3	1	5	ASP	ASP	GLY	GLY	4	C	C	982 - 1003	3 - 24
4	1	5	ASP	ASP	GLY	GLY	4	D	D	982 - 1003	3 - 24
1	2	5	GLY	GLY	VAL	VAL	4	A	A	1005 - 1032	26 - 53
2	2	5	GLY	GLY	VAL	VAL	4	B	B	1005 - 1032	26 - 53
3	2	5	GLY	GLY	VAL	VAL	4	C	C	1005 - 1032	26 - 53
4	2	5	GLY	GLY	VAL	VAL	4	D	D	1005 - 1032	26 - 53
1	1	6	ASP	ASP	GLY	GLY	4	E	E	982 - 1003	3 - 24
2	1	6	ASP	ASP	GLY	GLY	4	F	F	982 - 1003	3 - 24
3	1	6	ASP	ASP	GLY	GLY	4	G	G	982 - 1003	3 - 24
4	1	6	ASP	ASP	GLY	GLY	4	H	H	982 - 1003	3 - 24
1	2	6	GLY	GLY	VAL	VAL	4	E	E	1005 - 1032	26 - 53
2	2	6	GLY	GLY	VAL	VAL	4	F	F	1005 - 1032	26 - 53
3	2	6	GLY	GLY	VAL	VAL	4	G	G	1005 - 1032	26 - 53
4	2	6	GLY	GLY	VAL	VAL	4	H	H	1005 - 1032	26 - 53
1	1	7	ILE	ILE	ARG	ARG	4	A	A	1042 - 1092	63 - 113
2	1	7	ILE	ILE	ARG	ARG	4	B	B	1042 - 1092	63 - 113
3	1	7	ILE	ILE	ARG	ARG	4	C	C	1042 - 1092	63 - 113
4	1	7	ILE	ILE	ARG	ARG	4	D	D	1042 - 1092	63 - 113
1	1	8	ILE	ILE	ARG	ARG	4	E	E	1042 - 1092	63 - 113
2	1	8	ILE	ILE	ARG	ARG	4	F	F	1042 - 1092	63 - 113
3	1	8	ILE	ILE	ARG	ARG	4	G	G	1042 - 1092	63 - 113
4	1	8	ILE	ILE	ARG	ARG	4	H	H	1042 - 1092	63 - 113
1	1	9	ALA	ALA	LEU	LEU	4	A	A	1102 - 1170	123 - 191
2	1	9	ALA	ALA	LEU	LEU	4	B	B	1102 - 1170	123 - 191
3	1	9	ALA	ALA	LEU	LEU	4	C	C	1102 - 1170	123 - 191
4	1	9	ALA	ALA	LEU	LEU	4	D	D	1102 - 1170	123 - 191
1	1	10	ALA	ALA	LEU	LEU	4	E	E	1102 - 1170	123 - 191
2	1	10	ALA	ALA	LEU	LEU	4	F	F	1102 - 1170	123 - 191
3	1	10	ALA	ALA	LEU	LEU	4	G	G	1102 - 1170	123 - 191
4	1	10	ALA	ALA	LEU	LEU	4	H	H	1102 - 1170	123 - 191
1	1	11	LEU	LEU	SER	SER	4	A	A	1171 - 1279	192 - 300
2	1	11	LEU	LEU	SER	SER	4	B	B	1171 - 1279	192 - 300
3	1	11	LEU	LEU	SER	SER	4	C	C	1171 - 1279	192 - 300
4	1	11	LEU	LEU	SER	SER	4	D	D	1171 - 1279	192 - 300
1	1	12	LEU	LEU	SER	SER	4	E	E	1171 - 1279	192 - 300
2	1	12	LEU	LEU	SER	SER	4	F	F	1171 - 1279	192 - 300
3	1	12	LEU	LEU	SER	SER	4	G	G	1171 - 1279	192 - 300
4	1	12	LEU	LEU	SER	SER	4	H	H	1171 - 1279	192 - 300

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12

#1: Protein	Insulin-like growth factor 1 receptor / Insulin-like growth factor I receptor / IGF-I receptor Mass: 34607.758 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGF1R / Production host: unidentified baculovirus References: UniProt: P08069, receptor protein-tyrosine kinase
#2: Chemical	ChemComp-66A / 7-[cis-3-(azetidin-1-ylmethyl)cyclobutyl]-5-[3-(benzyloxy)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine Mass: 439.552 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₇H₂₉N₅O
#3: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.97 Å³/Da / Density % sol: 58.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 25% PEG8000, 0.1M MES PH6.25, 0.2 M AMMONIUM SULFATE, 4% GLYCEROL

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06SA / Wavelength: 0.97779 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2003

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97779 Å / Relative weight: 1

Reflection

Resolution: 2.2→40 Å / Num. obs: 147785 / % possible obs: 90.9 % / Redundancy: 3.5 % / R_merge(I) obs: 0.078 / Net I/av σ(I): 16.638 / Net I/σ(I): 9.8

Reflection shell

Resolution (Å)	R_merge(I) obs	Diffraction-ID	% possible all
2.2-2.28	0.413	1	78.5
2.28-2.37	0.304	1	78.6
2.37-2.48	0.238	1	81
2.48-2.61	0.19	1	86.9
2.61-2.77	0.147	1	91.8
2.77-2.99	0.118	1	95.9
2.99-3.29	0.097	1	98.3
3.29-3.76	0.079	1	99.2
3.76-4.74	0.064	1	99.4
4.74-40	0.054	1	99.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 0.491 / Cor.coef. F_o:F_c: 0.36

	Highest resolution	Lowest resolution
Rotation	4 Å	38.87 Å
Translation	4 Å	38.87 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	5.1.9999	refinement
PDB_EXTRACT	3.2	data extraction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.938 / SU B: 9.71 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2567 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.19

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2178	7403	5 %	RANDOM
R_work	0.194	-	-	-
obs	0.1952	140330	90.62 %	-

Solvent computation

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

Displacement parameters

B_iso max: 91.49 Å² / B_iso mean: 45.611 Å² / B_iso min: 17.99 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.08 Å²	0 Å²	0.05 Å²
2-	-	2.95 Å²	0 Å²
3-	-	-	-1.86 Å²

Refinement step

Cycle: final / Resolution: 2.2→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18975	0	380	551	19906
B_iso mean	-	-	50.34	42.78	-
Num. residues	-	-	-	-	2383

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	19811
X-RAY DIFFRACTION	r_angle_refined_deg	1.786	1.976	26749
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.148	5	2361
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.32	23.947	912
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.003	15	3476
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.621	15	144
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2827
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14988
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	9022
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	971
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.221	0.2	81
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.146	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	1.072	2	12277
X-RAY DIFFRACTION	r_mcangle_it	1.712	3	19094
X-RAY DIFFRACTION	r_scbond_it	2.227	4	8824
X-RAY DIFFRACTION	r_scangle_it	3.445	6	7623

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2331	TIGHT POSITIONAL	0.05	0.05
1	A	2331	TIGHT THERMAL	0.17	0.5
2	B	2331	TIGHT POSITIONAL	0.06	0.05
2	B	2331	TIGHT THERMAL	0.25	0.5
3	C	2359	TIGHT POSITIONAL	0.06	0.05
3	C	2359	TIGHT THERMAL	0.21	0.5
4	D	2396	TIGHT POSITIONAL	0.08	0.05
4	D	2396	TIGHT THERMAL	0.18	0.5
5	A	390	MEDIUM POSITIONAL	0.42	0.5
5	B	390	MEDIUM POSITIONAL	0.45	0.5
5	C	390	MEDIUM POSITIONAL	0.39	0.5
5	D	390	MEDIUM POSITIONAL	0.58	0.5
5	A	390	MEDIUM THERMAL	2.12	2
5	B	390	MEDIUM THERMAL	1.46	2
5	C	390	MEDIUM THERMAL	1.8	2
5	D	390	MEDIUM THERMAL	1.58	2
6	E	390	MEDIUM POSITIONAL	0.42	0.5
6	F	390	MEDIUM POSITIONAL	0.45	0.5
6	G	390	MEDIUM POSITIONAL	0.39	0.5
6	H	390	MEDIUM POSITIONAL	0.58	0.5
6	E	390	MEDIUM THERMAL	2.19	2
6	F	390	MEDIUM THERMAL	1.52	2
6	G	390	MEDIUM THERMAL	1.69	2
6	H	390	MEDIUM THERMAL	1.54	2
7	A	408	MEDIUM POSITIONAL	0.31	0.5
7	B	408	MEDIUM POSITIONAL	0.34	0.5
7	C	408	MEDIUM POSITIONAL	0.31	0.5
7	D	408	MEDIUM POSITIONAL	0.38	0.5
7	A	408	MEDIUM THERMAL	1.7	2
7	B	408	MEDIUM THERMAL	1.59	2
7	C	408	MEDIUM THERMAL	1.5	2
7	D	408	MEDIUM THERMAL	1.71	2
8	E	408	MEDIUM POSITIONAL	0.3	0.5
8	F	408	MEDIUM POSITIONAL	0.35	0.5
8	G	408	MEDIUM POSITIONAL	0.3	0.5
8	H	408	MEDIUM POSITIONAL	0.37	0.5
8	E	408	MEDIUM THERMAL	1.64	2
8	F	408	MEDIUM THERMAL	1.63	2
8	G	408	MEDIUM THERMAL	1.31	2
8	H	408	MEDIUM THERMAL	1.62	2
9	A	530	MEDIUM POSITIONAL	0.32	0.5
9	B	530	MEDIUM POSITIONAL	0.25	0.5
9	C	530	MEDIUM POSITIONAL	0.37	0.5
9	D	530	MEDIUM POSITIONAL	0.31	0.5
9	A	530	MEDIUM THERMAL	1.6	2
9	B	530	MEDIUM THERMAL	1.6	2
9	C	530	MEDIUM THERMAL	1.4	2
9	D	530	MEDIUM THERMAL	1.85	2
10	E	530	MEDIUM POSITIONAL	0.31	0.5
10	F	530	MEDIUM POSITIONAL	0.24	0.5
10	G	530	MEDIUM POSITIONAL	0.39	0.5
10	H	530	MEDIUM POSITIONAL	0.3	0.5
10	E	530	MEDIUM THERMAL	1.65	2
10	F	530	MEDIUM THERMAL	1.54	2
10	G	530	MEDIUM THERMAL	1.43	2
10	H	530	MEDIUM THERMAL	1.74	2
11	A	898	MEDIUM POSITIONAL	0.26	0.5
11	B	898	MEDIUM POSITIONAL	0.29	0.5
11	C	898	MEDIUM POSITIONAL	0.26	0.5
11	D	898	MEDIUM POSITIONAL	0.28	0.5
11	A	898	MEDIUM THERMAL	1.71	2
11	B	898	MEDIUM THERMAL	1.53	2
11	C	898	MEDIUM THERMAL	1.49	2
11	D	898	MEDIUM THERMAL	1.3	2
12	E	898	MEDIUM POSITIONAL	0.26	0.5
12	F	898	MEDIUM POSITIONAL	0.29	0.5
12	G	898	MEDIUM POSITIONAL	0.26	0.5
12	H	898	MEDIUM POSITIONAL	0.29	0.5
12	E	898	MEDIUM THERMAL	1.7	2
12	F	898	MEDIUM THERMAL	1.45	2
12	G	898	MEDIUM THERMAL	1.41	2
12	H	898	MEDIUM THERMAL	1.28	2

LS refinement shell

Resolution: 2.201→2.258 Å / Total num. of bins used: 20

	R_factor	Num. reflection
R_free	0.271	428
R_work	0.237	8563
all	-	8991

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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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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Phasing

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Processing

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About Yorodumi

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News

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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

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi