PDB-7pg8: NaV_Ae1/Sp1CTD_pore-ANT05 complex

ID or keywords:

Entry

Database: PDB / ID: 7pg8

Title

NaV_Ae1/Sp1CTD_pore-ANT05 complex

Components

ANT05 H12 fab fragment, heavy chain
ANT05 H12 fab fragment, light chain
Ion transport protein,Voltage-gated sodium channel

Keywords

MEMBRANE PROTEIN / ion channel membrane protein transport protein antibody complex

Function / homology

Function and homology information

voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / monoatomic cation channel activity / membrane => GO:0016020 / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Alkalilimnicola ehrlichii MLHE-1 (bacteria)

Ruegeria pomeroyi DSS-3 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 4.5 Å

Authors

Lolicato, M. / Arrigoni, C.

Funding support

United States, 1items

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Quaternary structure independent folding of voltage-gated ion channel pore domain subunits.
Authors: Arrigoni, C. / Lolicato, M. / Shaya, D. / Rohaim, A. / Findeisen, F. / Fong, L.K. / Colleran, C.M. / Dominik, P. / Kim, S.S. / Schuermann, J.P. / DeGrado, W.F. / Grabe, M. / Kossiakoff, A.A. / Minor Jr., D.L.

History

Deposition	Aug 13, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 8, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 15, 2022	Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jun 29, 2022	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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	7pg8.cif.gz	671.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7pg8.ent.gz	483 KB	Display	PDB format
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Validation report

Summary document	7pg8_validation.pdf.gz	547.9 KB	Display	wwPDB validaton report
Full document	7pg8_full_validation.pdf.gz	593.8 KB	Display
Data in XML	7pg8_validation.xml.gz	130.9 KB	Display
Data in CIF	7pg8_validation.cif.gz	180.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pg/7pg8 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/7pg8	HTTPS FTP

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Related structure data

Related structure data	7pgbC 7pgfC 7pggC 7pghC 7pgiC 5hk7S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2)

Deposited unit

P: ANT05 H12 fab fragment, light chain

M: ANT05 H12 fab fragment, light chain

V: ANT05 H12 fab fragment, light chain

S: ANT05 H12 fab fragment, light chain

G: ANT05 H12 fab fragment, light chain

D: ANT05 H12 fab fragment, light chain

J: ANT05 H12 fab fragment, light chain

A: ANT05 H12 fab fragment, light chain

B: ANT05 H12 fab fragment, heavy chain

F: ANT05 H12 fab fragment, heavy chain

I: ANT05 H12 fab fragment, heavy chain

L: ANT05 H12 fab fragment, heavy chain

N: ANT05 H12 fab fragment, heavy chain

R: ANT05 H12 fab fragment, heavy chain

U: ANT05 H12 fab fragment, heavy chain

X: ANT05 H12 fab fragment, heavy chain

C: Ion transport protein,Voltage-gated sodium channel

E: Ion transport protein,Voltage-gated sodium channel

H: Ion transport protein,Voltage-gated sodium channel

K: Ion transport protein,Voltage-gated sodium channel

O: Ion transport protein,Voltage-gated sodium channel

Q: Ion transport protein,Voltage-gated sodium channel

T: Ion transport protein,Voltage-gated sodium channel

W: Ion transport protein,Voltage-gated sodium channel

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

1

P: ANT05 H12 fab fragment, light chain

M: ANT05 H12 fab fragment, light chain

V: ANT05 H12 fab fragment, light chain

S: ANT05 H12 fab fragment, light chain

N: ANT05 H12 fab fragment, heavy chain

R: ANT05 H12 fab fragment, heavy chain

U: ANT05 H12 fab fragment, heavy chain

X: ANT05 H12 fab fragment, heavy chain

O: Ion transport protein,Voltage-gated sodium channel

Q: Ion transport protein,Voltage-gated sodium channel

T: Ion transport protein,Voltage-gated sodium channel

W: Ion transport protein,Voltage-gated sodium channel

defined by author
Evidence: gel filtration, light scattering
258 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: ANT05 H12 fab fragment, light chain

D: ANT05 H12 fab fragment, light chain

J: ANT05 H12 fab fragment, light chain

A: ANT05 H12 fab fragment, light chain

B: ANT05 H12 fab fragment, heavy chain

F: ANT05 H12 fab fragment, heavy chain

I: ANT05 H12 fab fragment, heavy chain

L: ANT05 H12 fab fragment, heavy chain

C: Ion transport protein,Voltage-gated sodium channel

E: Ion transport protein,Voltage-gated sodium channel

H: Ion transport protein,Voltage-gated sodium channel

K: Ion transport protein,Voltage-gated sodium channel

defined by author
258 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	127.175, 127.175, 445.206
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	78
Space group name H-M	P4₃

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	SER	SER	GLY	GLY	P	A	0 - 214	1 - 215
2	1	SER	SER	GLY	GLY	M	B	0 - 214	1 - 215
1	2	SER	SER	GLY	GLY	P	A	0 - 214	1 - 215
2	2	SER	SER	GLY	GLY	V	C	0 - 214	1 - 215
1	3	SER	SER	GLY	GLY	P	A	0 - 214	1 - 215
2	3	SER	SER	GLY	GLY	S	D	0 - 214	1 - 215
1	4	SER	SER	GLY	GLY	P	A	0 - 214	1 - 215
2	4	SER	SER	GLY	GLY	G	E	0 - 214	1 - 215
1	5	SER	SER	GLY	GLY	P	A	0 - 214	1 - 215
2	5	SER	SER	GLY	GLY	D	F	0 - 214	1 - 215
1	6	SER	SER	GLY	GLY	P	A	0 - 214	1 - 215
2	6	SER	SER	GLY	GLY	J	G	0 - 214	1 - 215
1	7	SER	SER	GLY	GLY	P	A	0 - 214	1 - 215
2	7	SER	SER	GLY	GLY	A	H	0 - 214	1 - 215
1	8	SER	SER	GLY	GLY	M	B	0 - 214	1 - 215
2	8	SER	SER	GLY	GLY	V	C	0 - 214	1 - 215
1	9	SER	SER	GLY	GLY	M	B	0 - 214	1 - 215
2	9	SER	SER	GLY	GLY	S	D	0 - 214	1 - 215
1	10	SER	SER	GLY	GLY	M	B	0 - 214	1 - 215
2	10	SER	SER	GLY	GLY	G	E	0 - 214	1 - 215
1	11	SER	SER	GLY	GLY	M	B	0 - 214	1 - 215
2	11	SER	SER	GLY	GLY	D	F	0 - 214	1 - 215
1	12	SER	SER	GLY	GLY	M	B	0 - 214	1 - 215
2	12	SER	SER	GLY	GLY	J	G	0 - 214	1 - 215
1	13	SER	SER	GLY	GLY	M	B	0 - 214	1 - 215
2	13	SER	SER	GLY	GLY	A	H	0 - 214	1 - 215
1	14	SER	SER	GLY	GLY	V	C	0 - 214	1 - 215
2	14	SER	SER	GLY	GLY	S	D	0 - 214	1 - 215
1	15	SER	SER	GLY	GLY	V	C	0 - 214	1 - 215
2	15	SER	SER	GLY	GLY	G	E	0 - 214	1 - 215
1	16	SER	SER	GLY	GLY	V	C	0 - 214	1 - 215
2	16	SER	SER	GLY	GLY	D	F	0 - 214	1 - 215
1	17	SER	SER	GLY	GLY	V	C	0 - 214	1 - 215
2	17	SER	SER	GLY	GLY	J	G	0 - 214	1 - 215
1	18	SER	SER	GLY	GLY	V	C	0 - 214	1 - 215
2	18	SER	SER	GLY	GLY	A	H	0 - 214	1 - 215
1	19	SER	SER	GLY	GLY	S	D	0 - 214	1 - 215
2	19	SER	SER	GLY	GLY	G	E	0 - 214	1 - 215
1	20	SER	SER	GLY	GLY	S	D	0 - 214	1 - 215
2	20	SER	SER	GLY	GLY	D	F	0 - 214	1 - 215
1	21	SER	SER	GLY	GLY	S	D	0 - 214	1 - 215
2	21	SER	SER	GLY	GLY	J	G	0 - 214	1 - 215
1	22	SER	SER	GLY	GLY	S	D	0 - 214	1 - 215
2	22	SER	SER	GLY	GLY	A	H	0 - 214	1 - 215
1	23	SER	SER	GLY	GLY	G	E	0 - 214	1 - 215
2	23	SER	SER	GLY	GLY	D	F	0 - 214	1 - 215
1	24	SER	SER	GLY	GLY	G	E	0 - 214	1 - 215
2	24	SER	SER	GLY	GLY	J	G	0 - 214	1 - 215
1	25	SER	SER	GLY	GLY	G	E	0 - 214	1 - 215
2	25	SER	SER	GLY	GLY	A	H	0 - 214	1 - 215
1	26	SER	SER	GLY	GLY	D	F	0 - 214	1 - 215
2	26	SER	SER	GLY	GLY	J	G	0 - 214	1 - 215
1	27	SER	SER	GLY	GLY	D	F	0 - 214	1 - 215
2	27	SER	SER	GLY	GLY	A	H	0 - 214	1 - 215
1	28	SER	SER	GLY	GLY	J	G	0 - 214	1 - 215
2	28	SER	SER	GLY	GLY	A	H	0 - 214	1 - 215
1	29	VAL	VAL	PRO	PRO	B	I	2 - 218	5 - 225
2	29	VAL	VAL	PRO	PRO	F	J	2 - 218	5 - 225
1	30	VAL	VAL	PRO	PRO	B	I	2 - 218	5 - 225
2	30	VAL	VAL	PRO	PRO	I	K	2 - 218	5 - 225
1	31	VAL	VAL	PRO	PRO	B	I	2 - 218	5 - 225
2	31	VAL	VAL	PRO	PRO	L	L	2 - 218	5 - 225
1	32	VAL	VAL	PRO	PRO	B	I	2 - 218	5 - 225
2	32	VAL	VAL	PRO	PRO	N	M	2 - 218	5 - 225
1	33	VAL	VAL	PRO	PRO	B	I	2 - 218	5 - 225
2	33	VAL	VAL	PRO	PRO	R	N	2 - 218	5 - 225
1	34	VAL	VAL	PRO	PRO	B	I	2 - 218	5 - 225
2	34	VAL	VAL	PRO	PRO	U	O	2 - 218	5 - 225
1	35	VAL	VAL	PRO	PRO	B	I	2 - 218	5 - 225
2	35	VAL	VAL	PRO	PRO	X	P	2 - 218	5 - 225
1	36	VAL	VAL	PRO	PRO	F	J	2 - 218	5 - 225
2	36	VAL	VAL	PRO	PRO	I	K	2 - 218	5 - 225
1	37	VAL	VAL	PRO	PRO	F	J	2 - 218	5 - 225
2	37	VAL	VAL	PRO	PRO	L	L	2 - 218	5 - 225
1	38	VAL	VAL	PRO	PRO	F	J	2 - 218	5 - 225
2	38	VAL	VAL	PRO	PRO	N	M	2 - 218	5 - 225
1	39	VAL	VAL	PRO	PRO	F	J	2 - 218	5 - 225
2	39	VAL	VAL	PRO	PRO	R	N	2 - 218	5 - 225
1	40	VAL	VAL	PRO	PRO	F	J	2 - 218	5 - 225
2	40	VAL	VAL	PRO	PRO	U	O	2 - 218	5 - 225
1	41	VAL	VAL	PRO	PRO	F	J	2 - 218	5 - 225
2	41	VAL	VAL	PRO	PRO	X	P	2 - 218	5 - 225
1	42	VAL	VAL	PRO	PRO	I	K	2 - 218	5 - 225
2	42	VAL	VAL	PRO	PRO	L	L	2 - 218	5 - 225
1	43	VAL	VAL	PRO	PRO	I	K	2 - 218	5 - 225
2	43	VAL	VAL	PRO	PRO	N	M	2 - 218	5 - 225
1	44	VAL	VAL	PRO	PRO	I	K	2 - 218	5 - 225
2	44	VAL	VAL	PRO	PRO	R	N	2 - 218	5 - 225
1	45	VAL	VAL	PRO	PRO	I	K	2 - 218	5 - 225
2	45	VAL	VAL	PRO	PRO	U	O	2 - 218	5 - 225
1	46	VAL	VAL	PRO	PRO	I	K	2 - 218	5 - 225
2	46	VAL	VAL	PRO	PRO	X	P	2 - 218	5 - 225
1	47	VAL	VAL	PRO	PRO	L	L	2 - 218	5 - 225
2	47	VAL	VAL	PRO	PRO	N	M	2 - 218	5 - 225
1	48	VAL	VAL	PRO	PRO	L	L	2 - 218	5 - 225
2	48	VAL	VAL	PRO	PRO	R	N	2 - 218	5 - 225
1	49	VAL	VAL	PRO	PRO	L	L	2 - 218	5 - 225
2	49	VAL	VAL	PRO	PRO	U	O	2 - 218	5 - 225
1	50	VAL	VAL	PRO	PRO	L	L	2 - 218	5 - 225
2	50	VAL	VAL	PRO	PRO	X	P	2 - 218	5 - 225
1	51	VAL	VAL	PRO	PRO	N	M	2 - 218	5 - 225
2	51	VAL	VAL	PRO	PRO	R	N	2 - 218	5 - 225
1	52	VAL	VAL	PRO	PRO	N	M	2 - 218	5 - 225
2	52	VAL	VAL	PRO	PRO	U	O	2 - 218	5 - 225
1	53	VAL	VAL	PRO	PRO	N	M	2 - 218	5 - 225
2	53	VAL	VAL	PRO	PRO	X	P	2 - 218	5 - 225
1	54	VAL	VAL	PRO	PRO	R	N	2 - 218	5 - 225
2	54	VAL	VAL	PRO	PRO	U	O	2 - 218	5 - 225
1	55	VAL	VAL	PRO	PRO	R	N	2 - 218	5 - 225
2	55	VAL	VAL	PRO	PRO	X	P	2 - 218	5 - 225
1	56	VAL	VAL	PRO	PRO	U	O	2 - 218	5 - 225
2	56	VAL	VAL	PRO	PRO	X	P	2 - 218	5 - 225
1	57	ALA	ALA	GLN	GLN	C	Q	146 - 269	10 - 133
2	57	ALA	ALA	GLN	GLN	E	R	146 - 269	10 - 133
1	58	ALA	ALA	LEU	LEU	C	Q	146 - 271	10 - 135
2	58	ALA	ALA	LEU	LEU	H	S	146 - 271	10 - 135
1	59	ALA	ALA	ARG	ARG	C	Q	146 - 270	10 - 134
2	59	ALA	ALA	ARG	ARG	K	T	146 - 270	10 - 134
1	60	ALA	ALA	LEU	LEU	C	Q	146 - 271	10 - 135
2	60	ALA	ALA	LEU	LEU	O	U	146 - 271	10 - 135
1	61	ALA	ALA	ILE	ILE	C	Q	146 - 267	10 - 131
2	61	ALA	ALA	ILE	ILE	Q	V	146 - 267	10 - 131
1	62	ALA	ALA	LEU	LEU	C	Q	146 - 271	10 - 135
2	62	ALA	ALA	LEU	LEU	T	W	146 - 271	10 - 135
1	63	ALA	ALA	ARG	ARG	C	Q	146 - 270	10 - 134
2	63	ALA	ALA	ARG	ARG	W	X	146 - 270	10 - 134
1	64	LEU	LEU	GLN	GLN	E	R	143 - 269	7 - 133
2	64	LEU	LEU	GLN	GLN	H	S	143 - 269	7 - 133
1	65	LEU	LEU	GLN	GLN	E	R	143 - 269	7 - 133
2	65	LEU	LEU	GLN	GLN	K	T	143 - 269	7 - 133
1	66	LEU	LEU	GLN	GLN	E	R	143 - 269	7 - 133
2	66	LEU	LEU	GLN	GLN	O	U	143 - 269	7 - 133
1	67	LEU	LEU	ILE	ILE	E	R	143 - 267	7 - 131
2	67	LEU	LEU	ILE	ILE	Q	V	143 - 267	7 - 131
1	68	LEU	LEU	GLN	GLN	E	R	143 - 269	7 - 133
2	68	LEU	LEU	GLN	GLN	T	W	143 - 269	7 - 133
1	69	LEU	LEU	GLN	GLN	E	R	143 - 269	7 - 133
2	69	LEU	LEU	GLN	GLN	W	X	143 - 269	7 - 133
1	70	LEU	LEU	ARG	ARG	H	S	143 - 270	7 - 134
2	70	LEU	LEU	ARG	ARG	K	T	143 - 270	7 - 134
1	71	LEU	LEU	ASN	ASN	H	S	143 - 272	7 - 136
2	71	LEU	LEU	ASN	ASN	O	U	143 - 272	7 - 136
1	72	LEU	LEU	ILE	ILE	H	S	143 - 267	7 - 131
2	72	LEU	LEU	ILE	ILE	Q	V	143 - 267	7 - 131
1	73	LEU	LEU	ASN	ASN	H	S	143 - 272	7 - 136
2	73	LEU	LEU	ASN	ASN	T	W	143 - 272	7 - 136
1	74	LEU	LEU	ARG	ARG	H	S	143 - 270	7 - 134
2	74	LEU	LEU	ARG	ARG	W	X	143 - 270	7 - 134
1	75	LEU	LEU	ARG	ARG	K	T	143 - 270	7 - 134
2	75	LEU	LEU	ARG	ARG	O	U	143 - 270	7 - 134
1	76	LEU	LEU	ILE	ILE	K	T	143 - 267	7 - 131
2	76	LEU	LEU	ILE	ILE	Q	V	143 - 267	7 - 131
1	77	LEU	LEU	ARG	ARG	K	T	143 - 270	7 - 134
2	77	LEU	LEU	ARG	ARG	T	W	143 - 270	7 - 134
1	78	LEU	LEU	LEU	LEU	K	T	143 - 271	7 - 135
2	78	LEU	LEU	LEU	LEU	W	X	143 - 271	7 - 135
1	79	LEU	LEU	ILE	ILE	O	U	143 - 267	7 - 131
2	79	LEU	LEU	ILE	ILE	Q	V	143 - 267	7 - 131
1	80	LEU	LEU	ASN	ASN	O	U	143 - 272	7 - 136
2	80	LEU	LEU	ASN	ASN	T	W	143 - 272	7 - 136
1	81	LEU	LEU	ARG	ARG	O	U	143 - 270	7 - 134
2	81	LEU	LEU	ARG	ARG	W	X	143 - 270	7 - 134
1	82	LEU	LEU	ILE	ILE	Q	V	143 - 267	7 - 131
2	82	LEU	LEU	ILE	ILE	T	W	143 - 267	7 - 131
1	83	LEU	LEU	ILE	ILE	Q	V	143 - 267	7 - 131
2	83	LEU	LEU	ILE	ILE	W	X	143 - 267	7 - 131
1	84	LEU	LEU	ARG	ARG	T	W	143 - 270	7 - 134
2	84	LEU	LEU	ARG	ARG	W	X	143 - 270	7 - 134

NCS ensembles :

#1: Antibody	ANT05 H12 fab fragment, light chain Mass: 23688.275 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	ANT05 H12 fab fragment, heavy chain Mass: 24651.496 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein	Ion transport protein,Voltage-gated sodium channel Mass: 16121.689 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alkalilimnicola ehrlichii MLHE-1 (bacteria), (gene. exp.) Ruegeria pomeroyi DSS-3 (bacteria) Strain: ATCC BAA-1101 / DSM 17681 / MLHE-1, ATCC 700808 / DSM 15171 / DSS-3 Gene: Mlg_0322, SPO0030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0ABW0, UniProt: F7IVA8

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.71 Å³/Da / Density % sol: 66.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 13% PEG4000, 2% propanol, 0.1M LiS04, 0.1 M 2-[(2-amino-2-oxoethyl)-(carboxymethyl)amino]acetic acid (ADA) pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 4.46→122.3 Å / Num. obs: 42377 / % possible obs: 98.31 % / Redundancy: 2 % / B_iso Wilson estimate: 254.59 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.031 / Net I/σ(I): 12.8
Reflection shell	Resolution: 4.46→4.62 Å / R_merge(I) obs: 1 / Num. unique obs: 3816 / CC_1/2: 0.442

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0	refinement
PDB_EXTRACT	3.27	data extraction
Aimless		data scaling
XDS		data reduction
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HK7

5hk7

Resolution: 4.5→15 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.907 / SU B: 196.06 / SU ML: 2.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.3517	2044	5.1 %	RANDOM
R_work	0.3031	-	-	-
obs	0.3056	38175	96.44 %	-

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 max: 653.57 Å² / B_iso mean: 163.129 Å² / B_iso min: 90.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.92 Å²	0 Å²	0 Å²
2-	-	5.92 Å²	0 Å²
3-	-	-	-11.83 Å²

Refinement step

Cycle: final / Resolution: 4.5→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22623	0	0	0	22623
Num. residues	-	-	-	-	4517

Refine LS restraints NCS

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

LS refinement shell

Resolution: 4.5→4.606 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.425	124	-
R_work	0.445	2377	-
all	-	2501	-
obs	-	-	89.55 %

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