PDB-4rau: crystal structure of RTOFab in complex with human PF4

ID or keywords:

Entry

Database: PDB / ID: 4rau

Title

crystal structure of RTOFab in complex with human PF4

Components

Platelet factor 4
RTOFab heavy chain
RTOFab light chain

Keywords

IMMUNE SYSTEM / RTO / PF4 / HIT / immunoglobulin / CXC chemokine / antibody / antigen / blood

Function / homology

Function and homology information

CXCR3 chemokine receptor binding / CXCR chemokine receptor binding / negative regulation of MHC class II biosynthetic process / killing by host of symbiont cells / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / leukocyte chemotaxis / chemokine activity / Chemokine receptors bind chemokines / defense response to protozoan ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.74 Å

Authors

Cai, Z. / Zhu, Z. / Liu, Q. / Greene, M.I.

Citation

Journal: To be Published
Title: crystal structure of RTOFab in complex with platelet factor 4
Authors: Cai, Z. / Zhu, Z. / Liu, Q. / Greene, M.I.

History

Deposition	Sep 11, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 16, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_sheet 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 / _struct_sheet.number_strands

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4rau.cif.gz	737.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4rau.ent.gz	613.6 KB	Display	PDB format
PDBx/mmJSON format	4rau.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4rau_validation.pdf.gz	607.4 KB	Display	wwPDB validaton report
Full document	4rau_full_validation.pdf.gz	682 KB	Display
Data in XML	4rau_validation.xml.gz	133.9 KB	Display
Data in CIF	4rau_validation.cif.gz	179 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ra/4rau ftp://data.pdbj.org/pub/pdb/validation_reports/ra/4rau	HTTPS FTP

-
Related structure data

Similar structure data	5d72-1 5wk3-3 3wih-1 5tru-2 4ffz-1 5c7x-2 1tpx-d 6txz-4 4i77-d 6ddv-d 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (6) #25 - Jan 2002 Thrombin similarity (1) #83 - Nov 2006 Fibrin similarity (1) #134 - Feb 2011 Integrin similarity (1) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (1) #75 - Mar 2006 Tissue Factor similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (6)
#25 - Jan 2002
Thrombin
similarity (1)
#83 - Nov 2006
Fibrin
similarity (1)
#134 - Feb 2011
Integrin
similarity (1)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (1)
#75 - Mar 2006
Tissue Factor
similarity (1)

Deposited unit

A: RTOFab light chain

B: RTOFab heavy chain

C: Platelet factor 4

D: RTOFab light chain

E: RTOFab heavy chain

F: Platelet factor 4

G: RTOFab light chain

H: RTOFab heavy chain

I: Platelet factor 4

J: RTOFab light chain

K: RTOFab heavy chain

L: Platelet factor 4

M: RTOFab light chain

N: RTOFab heavy chain

O: Platelet factor 4

P: RTOFab light chain

Q: RTOFab heavy chain

R: Platelet factor 4

S: RTOFab light chain

T: RTOFab heavy chain

U: Platelet factor 4

V: RTOFab light chain

W: RTOFab heavy chain

X: Platelet factor 4

439 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RTOFab light chain

B: RTOFab heavy chain

C: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: RTOFab light chain

E: RTOFab heavy chain

F: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: RTOFab light chain

H: RTOFab heavy chain

I: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

J: RTOFab light chain

K: RTOFab heavy chain

L: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

M: RTOFab light chain

N: RTOFab heavy chain

O: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

P: RTOFab light chain

Q: RTOFab heavy chain

R: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

S: RTOFab light chain

T: RTOFab heavy chain

U: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

V: RTOFab light chain

W: RTOFab heavy chain

X: Platelet factor 4

defined by author
54.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	161.424, 171.873, 208.159
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

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	ASP	ASP	ASN	ASN	A	A	3 - 214	1 - 212
2	1	ASP	ASP	ASN	ASN	D	D	3 - 214	1 - 212
1	2	ASP	ASP	ASN	ASN	A	A	3 - 214	1 - 212
2	2	ASP	ASP	ASN	ASN	G	G	3 - 214	1 - 212
1	3	ASP	ASP	ASN	ASN	A	A	3 - 214	1 - 212
2	3	ASP	ASP	ASN	ASN	J	J	3 - 214	1 - 212
1	4	ASP	ASP	ASN	ASN	A	A	3 - 214	1 - 212
2	4	ASP	ASP	ASN	ASN	M	M	3 - 214	1 - 212
1	5	ASP	ASP	ASN	ASN	A	A	3 - 214	1 - 212
2	5	ASP	ASP	ASN	ASN	P	P	3 - 214	1 - 212
1	6	ASP	ASP	ASN	ASN	A	A	3 - 214	1 - 212
2	6	ASP	ASP	ASN	ASN	S	S	3 - 214	1 - 212
1	7	ASP	ASP	ASN	ASN	A	A	3 - 214	1 - 212
2	7	ASP	ASP	ASN	ASN	V	V	3 - 214	1 - 212
1	8	GLU	GLU	SER	SER	B	B	3 - 221	1 - 219
2	8	GLU	GLU	SER	SER	E	E	3 - 221	1 - 219
1	9	GLU	GLU	SER	SER	B	B	3 - 221	1 - 219
2	9	GLU	GLU	SER	SER	H	H	3 - 221	1 - 219
1	10	GLU	GLU	SER	SER	B	B	3 - 221	1 - 219
2	10	GLU	GLU	SER	SER	K	K	3 - 221	1 - 219
1	11	GLU	GLU	SER	SER	B	B	3 - 221	1 - 219
2	11	GLU	GLU	SER	SER	N	N	3 - 221	1 - 219
1	12	GLU	GLU	SER	SER	B	B	3 - 221	1 - 219
2	12	GLU	GLU	SER	SER	Q	Q	3 - 221	1 - 219
1	13	GLU	GLU	SER	SER	B	B	3 - 221	1 - 219
2	13	GLU	GLU	SER	SER	T	T	3 - 221	1 - 219
1	14	GLU	GLU	SER	SER	B	B	3 - 221	1 - 219
2	14	GLU	GLU	SER	SER	W	W	3 - 221	1 - 219
1	15	GLU	GLU	LEU	LEU	C	C	4 - 68	4 - 68
2	15	GLU	GLU	LEU	LEU	F	F	4 - 68	4 - 68
1	16	GLU	GLU	LEU	LEU	C	C	4 - 67	4 - 67
2	16	GLU	GLU	LEU	LEU	I	I	4 - 67	4 - 67
1	17	GLU	GLU	LEU	LEU	C	C	4 - 68	4 - 68
2	17	GLU	GLU	LEU	LEU	L	L	4 - 68	4 - 68
1	18	GLU	GLU	LEU	LEU	C	C	4 - 68	4 - 68
2	18	GLU	GLU	LEU	LEU	O	O	4 - 68	4 - 68
1	19	GLU	GLU	LEU	LEU	C	C	4 - 68	4 - 68
2	19	GLU	GLU	LEU	LEU	R	R	4 - 68	4 - 68
1	20	GLU	GLU	LEU	LEU	C	C	4 - 68	4 - 68
2	20	GLU	GLU	LEU	LEU	U	U	4 - 68	4 - 68
1	21	GLU	GLU	LEU	LEU	C	C	4 - 67	4 - 67
2	21	GLU	GLU	LEU	LEU	X	X	4 - 67	4 - 67
1	22	ASP	ASP	ASN	ASN	D	D	3 - 214	1 - 212
2	22	ASP	ASP	ASN	ASN	G	G	3 - 214	1 - 212
1	23	ASP	ASP	ASN	ASN	D	D	3 - 214	1 - 212
2	23	ASP	ASP	ASN	ASN	J	J	3 - 214	1 - 212
1	24	ASP	ASP	ASN	ASN	D	D	3 - 214	1 - 212
2	24	ASP	ASP	ASN	ASN	M	M	3 - 214	1 - 212
1	25	ASP	ASP	ASN	ASN	D	D	3 - 214	1 - 212
2	25	ASP	ASP	ASN	ASN	P	P	3 - 214	1 - 212
1	26	ASP	ASP	ASN	ASN	D	D	3 - 214	1 - 212
2	26	ASP	ASP	ASN	ASN	S	S	3 - 214	1 - 212
1	27	ASP	ASP	ASN	ASN	D	D	3 - 214	1 - 212
2	27	ASP	ASP	ASN	ASN	V	V	3 - 214	1 - 212
1	28	GLU	GLU	SER	SER	E	E	3 - 221	1 - 219
2	28	GLU	GLU	SER	SER	H	H	3 - 221	1 - 219
1	29	GLU	GLU	SER	SER	E	E	3 - 221	1 - 219
2	29	GLU	GLU	SER	SER	K	K	3 - 221	1 - 219
1	30	GLU	GLU	SER	SER	E	E	3 - 221	1 - 219
2	30	GLU	GLU	SER	SER	N	N	3 - 221	1 - 219
1	31	GLU	GLU	SER	SER	E	E	3 - 221	1 - 219
2	31	GLU	GLU	SER	SER	Q	Q	3 - 221	1 - 219
1	32	GLU	GLU	SER	SER	E	E	3 - 221	1 - 219
2	32	GLU	GLU	SER	SER	T	T	3 - 221	1 - 219
1	33	GLU	GLU	SER	SER	E	E	3 - 221	1 - 219
2	33	GLU	GLU	SER	SER	W	W	3 - 221	1 - 219
1	34	GLU	GLU	LEU	LEU	F	F	4 - 67	4 - 67
2	34	GLU	GLU	LEU	LEU	I	I	4 - 67	4 - 67
1	35	GLU	GLU	LEU	LEU	F	F	4 - 68	4 - 68
2	35	GLU	GLU	LEU	LEU	L	L	4 - 68	4 - 68
1	36	GLU	GLU	LEU	LEU	F	F	4 - 68	4 - 68
2	36	GLU	GLU	LEU	LEU	O	O	4 - 68	4 - 68
1	37	GLU	GLU	LEU	LEU	F	F	4 - 68	4 - 68
2	37	GLU	GLU	LEU	LEU	R	R	4 - 68	4 - 68
1	38	GLU	GLU	LEU	LEU	F	F	4 - 68	4 - 68
2	38	GLU	GLU	LEU	LEU	U	U	4 - 68	4 - 68
1	39	GLU	GLU	LEU	LEU	F	F	4 - 67	4 - 67
2	39	GLU	GLU	LEU	LEU	X	X	4 - 67	4 - 67
1	40	ASP	ASP	ASN	ASN	G	G	3 - 214	1 - 212
2	40	ASP	ASP	ASN	ASN	J	J	3 - 214	1 - 212
1	41	ASP	ASP	ASN	ASN	G	G	3 - 214	1 - 212
2	41	ASP	ASP	ASN	ASN	M	M	3 - 214	1 - 212
1	42	ASP	ASP	ASN	ASN	G	G	3 - 214	1 - 212
2	42	ASP	ASP	ASN	ASN	P	P	3 - 214	1 - 212
1	43	ASP	ASP	ASN	ASN	G	G	3 - 214	1 - 212
2	43	ASP	ASP	ASN	ASN	S	S	3 - 214	1 - 212
1	44	ASP	ASP	ASN	ASN	G	G	3 - 214	1 - 212
2	44	ASP	ASP	ASN	ASN	V	V	3 - 214	1 - 212
1	45	GLU	GLU	SER	SER	H	H	3 - 221	1 - 219
2	45	GLU	GLU	SER	SER	K	K	3 - 221	1 - 219
1	46	GLU	GLU	SER	SER	H	H	3 - 221	1 - 219
2	46	GLU	GLU	SER	SER	N	N	3 - 221	1 - 219
1	47	GLU	GLU	SER	SER	H	H	3 - 221	1 - 219
2	47	GLU	GLU	SER	SER	Q	Q	3 - 221	1 - 219
1	48	GLU	GLU	SER	SER	H	H	3 - 221	1 - 219
2	48	GLU	GLU	SER	SER	T	T	3 - 221	1 - 219
1	49	GLU	GLU	SER	SER	H	H	3 - 221	1 - 219
2	49	GLU	GLU	SER	SER	W	W	3 - 221	1 - 219
1	50	GLU	GLU	LEU	LEU	I	I	4 - 67	4 - 67
2	50	GLU	GLU	LEU	LEU	L	L	4 - 67	4 - 67
1	51	GLU	GLU	LEU	LEU	I	I	4 - 67	4 - 67
2	51	GLU	GLU	LEU	LEU	O	O	4 - 67	4 - 67
1	52	GLU	GLU	LEU	LEU	I	I	4 - 67	4 - 67
2	52	GLU	GLU	LEU	LEU	R	R	4 - 67	4 - 67
1	53	GLU	GLU	LEU	LEU	I	I	4 - 67	4 - 67
2	53	GLU	GLU	LEU	LEU	U	U	4 - 67	4 - 67
1	54	GLU	GLU	GLU	GLU	I	I	4 - 69	4 - 69
2	54	GLU	GLU	GLU	GLU	X	X	4 - 69	4 - 69
1	55	ASP	ASP	ASN	ASN	J	J	3 - 214	1 - 212
2	55	ASP	ASP	ASN	ASN	M	M	3 - 214	1 - 212
1	56	ASP	ASP	ASN	ASN	J	J	3 - 214	1 - 212
2	56	ASP	ASP	ASN	ASN	P	P	3 - 214	1 - 212
1	57	ASP	ASP	ASN	ASN	J	J	3 - 214	1 - 212
2	57	ASP	ASP	ASN	ASN	S	S	3 - 214	1 - 212
1	58	ASP	ASP	ASN	ASN	J	J	3 - 214	1 - 212
2	58	ASP	ASP	ASN	ASN	V	V	3 - 214	1 - 212
1	59	GLU	GLU	SER	SER	K	K	3 - 221	1 - 219
2	59	GLU	GLU	SER	SER	N	N	3 - 221	1 - 219
1	60	GLU	GLU	SER	SER	K	K	3 - 221	1 - 219
2	60	GLU	GLU	SER	SER	Q	Q	3 - 221	1 - 219
1	61	GLU	GLU	SER	SER	K	K	3 - 221	1 - 219
2	61	GLU	GLU	SER	SER	T	T	3 - 221	1 - 219
1	62	GLU	GLU	SER	SER	K	K	3 - 221	1 - 219
2	62	GLU	GLU	SER	SER	W	W	3 - 221	1 - 219
1	63	GLU	GLU	LEU	LEU	L	L	4 - 68	4 - 68
2	63	GLU	GLU	LEU	LEU	O	O	4 - 68	4 - 68
1	64	GLU	GLU	LEU	LEU	L	L	4 - 68	4 - 68
2	64	GLU	GLU	LEU	LEU	R	R	4 - 68	4 - 68
1	65	GLU	GLU	LEU	LEU	L	L	4 - 68	4 - 68
2	65	GLU	GLU	LEU	LEU	U	U	4 - 68	4 - 68
1	66	GLU	GLU	LEU	LEU	L	L	4 - 67	4 - 67
2	66	GLU	GLU	LEU	LEU	X	X	4 - 67	4 - 67
1	67	ASP	ASP	ASN	ASN	M	M	3 - 214	1 - 212
2	67	ASP	ASP	ASN	ASN	P	P	3 - 214	1 - 212
1	68	ASP	ASP	ASN	ASN	M	M	3 - 214	1 - 212
2	68	ASP	ASP	ASN	ASN	S	S	3 - 214	1 - 212
1	69	ASP	ASP	ASN	ASN	M	M	3 - 214	1 - 212
2	69	ASP	ASP	ASN	ASN	V	V	3 - 214	1 - 212
1	70	GLU	GLU	SER	SER	N	N	3 - 221	1 - 219
2	70	GLU	GLU	SER	SER	Q	Q	3 - 221	1 - 219
1	71	GLU	GLU	SER	SER	N	N	3 - 221	1 - 219
2	71	GLU	GLU	SER	SER	T	T	3 - 221	1 - 219
1	72	GLU	GLU	SER	SER	N	N	3 - 221	1 - 219
2	72	GLU	GLU	SER	SER	W	W	3 - 221	1 - 219
1	73	GLU	GLU	LEU	LEU	O	O	4 - 68	4 - 68
2	73	GLU	GLU	LEU	LEU	R	R	4 - 68	4 - 68
1	74	GLU	GLU	LEU	LEU	O	O	4 - 68	4 - 68
2	74	GLU	GLU	LEU	LEU	U	U	4 - 68	4 - 68
1	75	GLU	GLU	LEU	LEU	O	O	4 - 67	4 - 67
2	75	GLU	GLU	LEU	LEU	X	X	4 - 67	4 - 67
1	76	ASP	ASP	ASN	ASN	P	P	3 - 214	1 - 212
2	76	ASP	ASP	ASN	ASN	S	S	3 - 214	1 - 212
1	77	ASP	ASP	ASN	ASN	P	P	3 - 214	1 - 212
2	77	ASP	ASP	ASN	ASN	V	V	3 - 214	1 - 212
1	78	GLU	GLU	SER	SER	Q	Q	3 - 221	1 - 219
2	78	GLU	GLU	SER	SER	T	T	3 - 221	1 - 219
1	79	GLU	GLU	SER	SER	Q	Q	3 - 221	1 - 219
2	79	GLU	GLU	SER	SER	W	W	3 - 221	1 - 219
1	80	GLU	GLU	LEU	LEU	R	R	4 - 68	4 - 68
2	80	GLU	GLU	LEU	LEU	U	U	4 - 68	4 - 68
1	81	GLU	GLU	LEU	LEU	R	R	4 - 67	4 - 67
2	81	GLU	GLU	LEU	LEU	X	X	4 - 67	4 - 67
1	82	ASP	ASP	ASN	ASN	S	S	3 - 214	1 - 212
2	82	ASP	ASP	ASN	ASN	V	V	3 - 214	1 - 212
1	83	GLU	GLU	SER	SER	T	T	3 - 221	1 - 219
2	83	GLU	GLU	SER	SER	W	W	3 - 221	1 - 219
1	84	GLU	GLU	LEU	LEU	U	U	4 - 67	4 - 67
2	84	GLU	GLU	LEU	LEU	X	X	4 - 67	4 - 67

NCS ensembles :

#1: Antibody	RTOFab light chain Mass: 23383.781 Da / Num. of mol.: 8 / Fragment: UNP residues 32-101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody	RTOFab heavy chain Mass: 23653.461 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein	Platelet factor 4 / PF-4 / C-X-C motif chemokine 4 / Iroplact / Oncostatin-A / Platelet factor 4 / short form Mass: 7782.195 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PF4, CXCL4, SCYB4 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P02776
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.24 Å³/Da / Density % sol: 61.99 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, pH 6.5, 25% w/v Polyethylene glycol 3350., VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X4A / Wavelength: 2.07 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2014

Radiation

Monochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 2.07 Å / Relative weight: 1

Reflection

Resolution: 3.74→50 Å / Num. all: 60619 / Num. obs: 60223 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
3.75-3.81	25.6	0	2.9	1	98.9
3.81-3.88	25.6	0	4.2	1	98.6
3.88-3.96	25.5	0.965	5.6	1	98.6
3.96-4.04	25.9	0	4.6	1	99.1
4.04-4.13	26.2	0.765	7.1	1	99.3
4.13-4.22	26.5	0.589	9	1	99.1

-
Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.8.0049	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.74→50 Å / Cor.coef. F_o:F_c: 0.902 / Cor.coef. F_o:F_c free: 0.887 / SU B: 38.049 / SU ML: 0.511 / Cross valid method: THROUGHOUT / ESU R Free: 0.792 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28444	3011	5 %	RANDOM
R_work	0.24326	-	-	-
obs	0.24533	56670	98.51 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 136.355 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.43 Å²	0 Å²	0 Å²
2-	-	8.55 Å²	0 Å²
3-	-	-	-6.11 Å²

Refinement step

Cycle: LAST / Resolution: 3.74→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30074	0	0	0	30074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.02	30794
X-RAY DIFFRACTION	r_bond_other_d	0.004	0.02	28145
X-RAY DIFFRACTION	r_angle_refined_deg	1.278	1.96	41909
X-RAY DIFFRACTION	r_angle_other_deg	1.081	3	65115
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.304	5	3946
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.67	23.738	1137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.259	15	4920
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.297	15	144
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	4784
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	34666
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	6786
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	6.095	13.814	15856
X-RAY DIFFRACTION	r_mcbond_other	6.093	13.814	15855
X-RAY DIFFRACTION	r_mcangle_it	10.054	20.715	19778
X-RAY DIFFRACTION	r_mcangle_other	10.492	20.227	19779
X-RAY DIFFRACTION	r_scbond_it	5.378	14.028	14938
X-RAY DIFFRACTION	r_scbond_other	5.988	13.843	14939
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	10.233	20.562	22139
X-RAY DIFFRACTION	r_long_range_B_refined	15.678		33077
X-RAY DIFFRACTION	r_long_range_B_other	15.677		33076
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	11640	0.05
1	2	D	11640	0.05
2	1	A	11566	0.06
2	2	G	11566	0.06
3	1	A	11476	0.07
3	2	J	11476	0.07
4	1	A	11523	0.07
4	2	M	11523	0.07
5	1	A	11590	0.07
5	2	P	11590	0.07
6	1	A	11479	0.07
6	2	S	11479	0.07
7	1	A	11489	0.07
7	2	V	11489	0.07
8	1	B	11276	0.04
8	2	E	11276	0.04
9	1	B	11342	0.03
9	2	H	11342	0.03
10	1	B	11251	0.04
10	2	K	11251	0.04
11	1	B	11262	0.04
11	2	N	11262	0.04
12	1	B	11269	0.04
12	2	Q	11269	0.04
13	1	B	11303	0.04
13	2	T	11303	0.04
14	1	B	11325	0.03
14	2	W	11325	0.03
15	1	C	3959	0.03
15	2	F	3959	0.03
16	1	C	3733	0.05
16	2	I	3733	0.05
17	1	C	3752	0.08
17	2	L	3752	0.08
18	1	C	3941	0.05
18	2	O	3941	0.05
19	1	C	3955	0.03
19	2	R	3955	0.03
20	1	C	3840	0.06
20	2	U	3840	0.06
21	1	C	3783	0.06
21	2	X	3783	0.06
22	1	D	11420	0.08
22	2	G	11420	0.08
23	1	D	11434	0.07
23	2	J	11434	0.07
24	1	D	11409	0.07
24	2	M	11409	0.07
25	1	D	11421	0.07
25	2	P	11421	0.07
26	1	D	11324	0.08
26	2	S	11324	0.08
27	1	D	11529	0.07
27	2	V	11529	0.07
28	1	E	11316	0.05
28	2	H	11316	0.05
29	1	E	11269	0.03
29	2	K	11269	0.03
30	1	E	11253	0.05
30	2	N	11253	0.05
31	1	E	11254	0.05
31	2	Q	11254	0.05
32	1	E	11291	0.04
32	2	T	11291	0.04
33	1	E	11317	0.04
33	2	W	11317	0.04
34	1	F	3740	0.05
34	2	I	3740	0.05
35	1	F	3748	0.08
35	2	L	3748	0.08
36	1	F	3939	0.06
36	2	O	3939	0.06
37	1	F	3960	0.03
37	2	R	3960	0.03
38	1	F	3831	0.07
38	2	U	3831	0.07
39	1	F	3781	0.06
39	2	X	3781	0.06
40	1	G	11486	0.07
40	2	J	11486	0.07
41	1	G	11425	0.07
41	2	M	11425	0.07
42	1	G	11429	0.07
42	2	P	11429	0.07
43	1	G	11465	0.07
43	2	S	11465	0.07
44	1	G	11544	0.07
44	2	V	11544	0.07
45	1	H	11297	0.04
45	2	K	11297	0.04
46	1	H	11295	0.04
46	2	N	11295	0.04
47	1	H	11288	0.04
47	2	Q	11288	0.04
48	1	H	11336	0.04
48	2	T	11336	0.04
49	1	H	11360	0.03
49	2	W	11360	0.03
50	1	I	3585	0.08
50	2	L	3585	0.08
51	1	I	3712	0.07
51	2	O	3712	0.07
52	1	I	3736	0.05
52	2	R	3736	0.05
53	1	I	3677	0.07
53	2	U	3677	0.07
54	1	I	3786	0.08
54	2	X	3786	0.08
55	1	J	11352	0.08
55	2	M	11352	0.08
56	1	J	11412	0.07
56	2	P	11412	0.07
57	1	J	11429	0.07
57	2	S	11429	0.07
58	1	J	11446	0.07
58	2	V	11446	0.07
59	1	K	11229	0.05
59	2	N	11229	0.05
60	1	K	11230	0.05
60	2	Q	11230	0.05
61	1	K	11290	0.04
61	2	T	11290	0.04
62	1	K	11317	0.03
62	2	W	11317	0.03
63	1	L	3738	0.09
63	2	O	3738	0.09
64	1	L	3746	0.08
64	2	R	3746	0.08
65	1	L	3698	0.09
65	2	U	3698	0.09
66	1	L	3645	0.08
66	2	X	3645	0.08
67	1	M	11449	0.07
67	2	P	11449	0.07
68	1	M	11441	0.07
68	2	S	11441	0.07
69	1	M	11471	0.07
69	2	V	11471	0.07
70	1	N	11266	0.05
70	2	Q	11266	0.05
71	1	N	11262	0.04
71	2	T	11262	0.04
72	1	N	11292	0.04
72	2	W	11292	0.04
73	1	O	3934	0.06
73	2	R	3934	0.06
74	1	O	3814	0.08
74	2	U	3814	0.08
75	1	O	3772	0.07
75	2	X	3772	0.07
76	1	P	11421	0.07
76	2	S	11421	0.07
77	1	P	11401	0.08
77	2	V	11401	0.08
78	1	Q	11273	0.05
78	2	T	11273	0.05
79	1	Q	11301	0.04
79	2	W	11301	0.04
80	1	R	3829	0.07
80	2	U	3829	0.07
81	1	R	3780	0.06
81	2	X	3780	0.06
82	1	S	11485	0.07
82	2	V	11485	0.07
83	1	T	11390	0.02
83	2	W	11390	0.02
84	1	U	3704	0.08
84	2	X	3704	0.08

LS refinement shell

Resolution: 3.739→3.836 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	223	-
R_work	0.356	4097	-
obs	-	-	97.98 %

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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