PDB-6s4s: CBDP35 Native structure

Basic information

• Entry: Database: PDB / ID: 6s4s
• Title: CBDP35 Native structure
• Components: (PlyP35) x 3
• Keywords: HYDROLASE / ----
• Function / homology: PSA endolysin, cell wall binding domain / PSA endolysin C-terminal cell wall binding domain / Peptidase M15C / D-alanyl-D-alanine carboxypeptidase / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / peptidase activity / MALONATE ION / PlyP35
• Biological species: Listeria phage P35 (virus)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
• Authors: Hermoso, J.A. / Bartual, S.G.
• Citation: Journal: To Be Published; Title: CBDP35 Native structure; Authors: Hermoso, J.A. / Bartual, S.G.

History

Deposition	Jun 28, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_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

Assembly

Deposited unit

A: PlyP35

B: PlyP35

C: PlyP35

D: PlyP35

E: PlyP35

F: PlyP35

G: PlyP35

H: PlyP35

I: PlyP35

J: PlyP35

L: PlyP35

K: PlyP35

hetero molecules

Summary:

• 194 kDa, 12 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	193,939	17
Polymers	193,429	12
Non-polymers	510	5
Water	25,815	1433

1

A: PlyP35

Summary:

• defined by author
• Evidence: gel filtration
• 16.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,157	1
Polymers	16,157	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

2

B: PlyP35

hetero molecules

Summary:

• defined by author
• 16.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,193	2
Polymers	16,091	1
Non-polymers	102	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

3

C: PlyP35

hetero molecules

Summary:

• defined by author
• 16.3 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,331	2
Polymers	16,229	1
Non-polymers	102	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

4

D: PlyP35

Summary:

• defined by author
• 16.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,091	1
Polymers	16,091	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

5

E: PlyP35

Summary:

• defined by author
• 16.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,091	1
Polymers	16,091	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

6

F: PlyP35

Summary:

• defined by author
• 16.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,091	1
Polymers	16,091	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

7

G: PlyP35

hetero molecules

Summary:

• defined by author
• 16.4 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,397	4
Polymers	16,091	1
Non-polymers	306	3
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

8

H: PlyP35

Summary:

• defined by author
• 16.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,091	1
Polymers	16,091	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

9

I: PlyP35

Summary:

• defined by author
• 16.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,091	1
Polymers	16,091	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

10

J: PlyP35

Summary:

• defined by author
• 16.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,229	1
Polymers	16,229	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

11

L: PlyP35

Summary:

• defined by author
• 16.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,091	1
Polymers	16,091	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

12

K: PlyP35

Summary:

• defined by author
• 16.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	16,091	1
Polymers	16,091	1
Non-polymers	0	0
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	333.321, 95.118, 83.846
Angle α, β, γ (deg.)	90.00, 90.33, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-507- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	A
2	4	E
1	5	A
2	5	F
1	6	A
2	6	G
1	7	A
2	7	H
1	8	A
2	8	I
1	9	A
2	9	J
1	10	A
2	10	L
1	11	A
2	11	K
1	12	B
2	12	C
1	13	B
2	13	D
1	14	B
2	14	E
1	15	B
2	15	F
1	16	B
2	16	G
1	17	B
2	17	H
1	18	B
2	18	I
1	19	B
2	19	J
1	20	B
2	20	L
1	21	B
2	21	K
1	22	C
2	22	D
1	23	C
2	23	E
1	24	C
2	24	F
1	25	C
2	25	G
1	26	C
2	26	H
1	27	C
2	27	I
1	28	C
2	28	J
1	29	C
2	29	L
1	30	C
2	30	K
1	31	D
2	31	E
1	32	D
2	32	F
1	33	D
2	33	G
1	34	D
2	34	H
1	35	D
2	35	I
1	36	D
2	36	J
1	37	D
2	37	L
1	38	D
2	38	K
1	39	E
2	39	F
1	40	E
2	40	G
1	41	E
2	41	H
1	42	E
2	42	I
1	43	E
2	43	J
1	44	E
2	44	L
1	45	E
2	45	K
1	46	F
2	46	G
1	47	F
2	47	H
1	48	F
2	48	I
1	49	F
2	49	J
1	50	F
2	50	L
1	51	F
2	51	K
1	52	G
2	52	H
1	53	G
2	53	I
1	54	G
2	54	J
1	55	G
2	55	L
1	56	G
2	56	K
1	57	H
2	57	I
1	58	H
2	58	J
1	59	H
2	59	L
1	60	H
2	60	K
1	61	I
2	61	J
1	62	I
2	62	L
1	63	I
2	63	K
1	64	J
2	64	L
1	65	J
2	65	K
1	66	L
2	66	K

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	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	1	MET	MET	LYS	LYS	B	B	153 - 290	1 - 138
1	2	HIS	HIS	ILE	ILE	A	A	152 - 289	1 - 138
2	2	HIS	HIS	ILE	ILE	C	C	152 - 289	1 - 138
1	3	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	3	MET	MET	LYS	LYS	D	D	153 - 290	1 - 138
1	4	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	4	MET	MET	LYS	LYS	E	E	153 - 290	1 - 138
1	5	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	5	MET	MET	LYS	LYS	F	F	153 - 290	1 - 138
1	6	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	6	MET	MET	LYS	LYS	G	G	153 - 290	1 - 138
1	7	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	7	MET	MET	LYS	LYS	H	H	153 - 290	1 - 138
1	8	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	8	MET	MET	LYS	LYS	I	I	153 - 290	1 - 138
1	9	MET	MET	ILE	ILE	A	A	154 - 289	3 - 138
2	9	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	10	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	10	MET	MET	LYS	LYS	L	K	153 - 290	1 - 138
1	11	MET	MET	LYS	LYS	A	A	153 - 290	2 - 139
2	11	MET	MET	LYS	LYS	K	L	153 - 290	1 - 138
1	12	MET	MET	ILE	ILE	B	B	153 - 289	1 - 137
2	12	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
1	13	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	13	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
1	14	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	14	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
1	15	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	15	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
1	16	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	16	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
1	17	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	17	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
1	18	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	18	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
1	19	MET	MET	ILE	ILE	B	B	154 - 289	2 - 137
2	19	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	20	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	20	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
1	21	MET	MET	LYS	LYS	B	B	153 - 291	1 - 139
2	21	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139
1	22	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	22	MET	MET	ILE	ILE	D	D	153 - 289	1 - 137
1	23	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	23	MET	MET	ILE	ILE	E	E	153 - 289	1 - 137
1	24	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	24	MET	MET	ILE	ILE	F	F	153 - 289	1 - 137
1	25	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	25	MET	MET	ILE	ILE	G	G	153 - 289	1 - 137
1	26	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	26	MET	MET	ILE	ILE	H	H	153 - 289	1 - 137
1	27	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	27	MET	MET	ILE	ILE	I	I	153 - 289	1 - 137
1	28	MET	MET	ILE	ILE	C	C	154 - 289	3 - 138
2	28	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	29	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	29	MET	MET	ILE	ILE	L	K	153 - 289	1 - 137
1	30	MET	MET	ILE	ILE	C	C	153 - 289	2 - 138
2	30	MET	MET	ILE	ILE	K	L	153 - 289	1 - 137
1	31	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
2	31	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
1	32	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
2	32	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
1	33	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
2	33	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
1	34	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
2	34	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
1	35	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
2	35	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
1	36	MET	MET	ILE	ILE	D	D	154 - 289	2 - 137
2	36	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	37	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
2	37	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
1	38	MET	MET	LYS	LYS	D	D	153 - 291	1 - 139
2	38	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139
1	39	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
2	39	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
1	40	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
2	40	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
1	41	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
2	41	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
1	42	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
2	42	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
1	43	MET	MET	ILE	ILE	E	E	154 - 289	2 - 137
2	43	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	44	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
2	44	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
1	45	MET	MET	LYS	LYS	E	E	153 - 291	1 - 139
2	45	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139
1	46	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
2	46	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
1	47	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
2	47	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
1	48	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
2	48	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
1	49	MET	MET	ILE	ILE	F	F	154 - 289	2 - 137
2	49	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	50	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
2	50	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
1	51	MET	MET	LYS	LYS	F	F	153 - 291	1 - 139
2	51	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139
1	52	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
2	52	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
1	53	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
2	53	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
1	54	MET	MET	ILE	ILE	G	G	154 - 289	2 - 137
2	54	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	55	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
2	55	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
1	56	MET	MET	LYS	LYS	G	G	153 - 291	1 - 139
2	56	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139
1	57	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
2	57	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
1	58	MET	MET	ILE	ILE	H	H	154 - 289	2 - 137
2	58	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	59	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
2	59	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
1	60	MET	MET	LYS	LYS	H	H	153 - 291	1 - 139
2	60	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139
1	61	MET	MET	ILE	ILE	I	I	154 - 289	2 - 137
2	61	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
1	62	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
2	62	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
1	63	MET	MET	LYS	LYS	I	I	153 - 291	1 - 139
2	63	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139
1	64	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
2	64	MET	MET	ILE	ILE	L	K	154 - 289	2 - 137
1	65	MET	MET	ILE	ILE	J	J	154 - 289	3 - 138
2	65	MET	MET	ILE	ILE	K	L	154 - 289	2 - 137
1	66	MET	MET	LYS	LYS	L	K	153 - 291	1 - 139
2	66	MET	MET	LYS	LYS	K	L	153 - 291	1 - 139

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

Components

#1: Protein

A PlyP35

Details:

Mass: 16156.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage P35 (virus) / Gene: ply
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A8ATR6

#2: Protein

B D E F G H I L K
PlyP35

Details:

Mass: 16090.521 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage P35 (virus) / Gene: ply
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A8ATR6

#3: Protein

C J PlyP35

Details:

Mass: 16228.669 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage P35 (virus) / Gene: ply
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A8ATR6

#4: Chemical

B-301 C-301 G-301 G-302 G-303
ChemComp-MLI / MALONATE ION / Malonic acid

Details:

Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₂O₄

#5: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 1433 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: N

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.45 ų/Da / Density % sol: 64.3 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 4M Sodium formate

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786 Å
• Detector: Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9786 Å / Relative weight: 1
• Reflection: Resolution: 2.15→47.56 Å / Num. obs: 142267 / % possible obs: 99.82 % / Redundancy: 6.8 % / R_merge(I) obs: 0.1147 / Net I/σ(I): 12.98
• Reflection shell: Resolution: 2.15→2.227 Å / Redundancy: 6.7 % / R_merge(I) obs: 0.9802 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 14110 / CC_1/2: 0.998 / % possible all: 99.89

Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S3Y

6s3y

Resolution: 2.15→47.6 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.948 / SU B: 4.958 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.21177	7164	5 %	RANDOM
Rwork	0.18556	-	-	-
obs	0.18689	135102	99.9 %	-

• 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: 38.252 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-2.54 Å2	0 Å2	0.23 Å2
2-	-	0.94 Å2	0 Å2
3-	-	-	1.6 Å2

Refinement step

Cycle: LAST / Resolution: 2.15→47.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13609	0	35	1433	15077

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	14025
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	12853
X-RAY DIFFRACTION	r_angle_refined_deg	1.611	1.643	18831
X-RAY DIFFRACTION	r_angle_other_deg	1.306	1.594	29874
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.457	5	1655
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.828	22.197	710
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.888	15	2519
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.915	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	1726
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	15465
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3195
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	3.624	3.769	6656
X-RAY DIFFRACTION	r_mcbond_other	3.624	3.769	6655
X-RAY DIFFRACTION	r_mcangle_it	5.188	5.634	8299
X-RAY DIFFRACTION	r_mcangle_other	5.188	5.635	8300
X-RAY DIFFRACTION	r_scbond_it	4.567	4.122	7369
X-RAY DIFFRACTION	r_scbond_other	4.553	4.122	7366
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.841	5.956	10533
X-RAY DIFFRACTION	r_long_range_B_refined	9.509	42.23	15738
X-RAY DIFFRACTION	r_long_range_B_other	9.51	42.22	15736
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	4405	0.09
1	2	B	4405	0.09
2	1	A	4481	0.08
2	2	C	4481	0.08
3	1	A	4491	0.07
3	2	D	4491	0.07
4	1	A	4471	0.07
4	2	E	4471	0.07
5	1	A	4453	0.08
5	2	F	4453	0.08
6	1	A	4495	0.08
6	2	G	4495	0.08
7	1	A	4464	0.08
7	2	H	4464	0.08
8	1	A	4438	0.09
8	2	I	4438	0.09
9	1	A	4436	0.08
9	2	J	4436	0.08
10	1	A	4410	0.1
10	2	L	4410	0.1
11	1	A	4465	0.08
11	2	K	4465	0.08
12	1	B	4365	0.1
12	2	C	4365	0.1
13	1	B	4454	0.09
13	2	D	4454	0.09
14	1	B	4453	0.09
14	2	E	4453	0.09
15	1	B	4466	0.08
15	2	F	4466	0.08
16	1	B	4441	0.09
16	2	G	4441	0.09
17	1	B	4392	0.1
17	2	H	4392	0.1
18	1	B	4391	0.1
18	2	I	4391	0.1
19	1	B	4396	0.08
19	2	J	4396	0.08
20	1	B	4404	0.1
20	2	L	4404	0.1
21	1	B	4441	0.1
21	2	K	4441	0.1
22	1	C	4409	0.09
22	2	D	4409	0.09
23	1	C	4407	0.09
23	2	E	4407	0.09
24	1	C	4393	0.09
24	2	F	4393	0.09
25	1	C	4409	0.09
25	2	G	4409	0.09
26	1	C	4432	0.09
26	2	H	4432	0.09
27	1	C	4389	0.1
27	2	I	4389	0.1
28	1	C	4423	0.08
28	2	J	4423	0.08
29	1	C	4360	0.1
29	2	L	4360	0.1
30	1	C	4377	0.1
30	2	K	4377	0.1
31	1	D	4526	0.06
31	2	E	4526	0.06
32	1	D	4516	0.07
32	2	F	4516	0.07
33	1	D	4467	0.09
33	2	G	4467	0.09
34	1	D	4423	0.09
34	2	H	4423	0.09
35	1	D	4473	0.09
35	2	I	4473	0.09
36	1	D	4413	0.09
36	2	J	4413	0.09
37	1	D	4429	0.1
37	2	L	4429	0.1
38	1	D	4458	0.09
38	2	K	4458	0.09
39	1	E	4535	0.07
39	2	F	4535	0.07
40	1	E	4446	0.1
40	2	G	4446	0.1
41	1	E	4417	0.09
41	2	H	4417	0.09
42	1	E	4491	0.08
42	2	I	4491	0.08
43	1	E	4405	0.09
43	2	J	4405	0.09
44	1	E	4433	0.1
44	2	L	4433	0.1
45	1	E	4461	0.09
45	2	K	4461	0.09
46	1	F	4432	0.1
46	2	G	4432	0.1
47	1	F	4401	0.09
47	2	H	4401	0.09
48	1	F	4438	0.09
48	2	I	4438	0.09
49	1	F	4417	0.08
49	2	J	4417	0.08
50	1	F	4407	0.1
50	2	L	4407	0.1
51	1	F	4482	0.09
51	2	K	4482	0.09
52	1	G	4475	0.09
52	2	H	4475	0.09
53	1	G	4458	0.09
53	2	I	4458	0.09
54	1	G	4458	0.07
54	2	J	4458	0.07
55	1	G	4476	0.1
55	2	L	4476	0.1
56	1	G	4492	0.09
56	2	K	4492	0.09
57	1	H	4379	0.1
57	2	I	4379	0.1
58	1	H	4423	0.07
58	2	J	4423	0.07
59	1	H	4389	0.11
59	2	L	4389	0.11
60	1	H	4431	0.09
60	2	K	4431	0.09
61	1	I	4360	0.1
61	2	J	4360	0.1
62	1	I	4443	0.09
62	2	L	4443	0.09
63	1	I	4433	0.1
63	2	K	4433	0.1
64	1	J	4373	0.1
64	2	L	4373	0.1
65	1	J	4469	0.07
65	2	K	4469	0.07
66	1	L	4467	0.1
66	2	K	4467	0.1

LS refinement shell

Resolution: 2.15→2.206 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.314	520	-
Rwork	0.278	9963	-
obs	-	-	99.95 %