PDB-8bfe: A dimeric de novo coiled-coil assembly: PK-2 (CC-TypeN-LaUbUcLd)

Basic information

• Entry: Database: PDB / ID: 8bfe
• Title: A dimeric de novo coiled-coil assembly: PK-2 (CC-TypeN-LaUbUcLd)
• Components: CC-TypeN-LaUbUcLd
• Keywords: DE NOVO PROTEIN / alpha-helical / LL core / Aib
• Biological species: synthetic construct (others)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.1 Å
• Authors: Kumar, P. / Paterson, N.G. / Woolfson, D.N.

Funding support

United Kingdom, 2items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/L01386X/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/R00661X/1	United Kingdom

• Citation: Journal: Nature / Year: 2022; Title: De novo design of discrete, stable 3 10 -helix peptide assemblies.; Authors: Kumar, P. / Paterson, N.G. / Clayden, J. / Woolfson, D.N.

History

Deposition	Oct 25, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release

Assembly

Deposited unit

A: CC-TypeN-LaUbUcLd

B: CC-TypeN-LaUbUcLd

C: CC-TypeN-LaUbUcLd

D: CC-TypeN-LaUbUcLd

E: CC-TypeN-LaUbUcLd

F: CC-TypeN-LaUbUcLd

G: CC-TypeN-LaUbUcLd

H: CC-TypeN-LaUbUcLd

I: CC-TypeN-LaUbUcLd

J: CC-TypeN-LaUbUcLd

K: CC-TypeN-LaUbUcLd

L: CC-TypeN-LaUbUcLd

M: CC-TypeN-LaUbUcLd

N: CC-TypeN-LaUbUcLd

O: CC-TypeN-LaUbUcLd

P: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• 55.5 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	55,489	44
Polymers	54,113	16
Non-polymers	1,376	28
Water	1,549	86

1

A: CC-TypeN-LaUbUcLd

hetero molecules

K: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• Evidence: equilibrium centrifugation
• 6.97 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,971	8
Polymers	6,764	2
Non-polymers	207	6
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_656	-x+3/2,y+1/2,-z+1	1

2

B: CC-TypeN-LaUbUcLd

hetero molecules

B: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• 6.98 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,980	8
Polymers	6,764	2
Non-polymers	216	6
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,y,-z	1

3

C: CC-TypeN-LaUbUcLd

D: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• 7.04 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	7,042	6
Polymers	6,764	2
Non-polymers	278	4
Water	36	2

Symmetry operations:

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

4

E: CC-TypeN-LaUbUcLd

hetero molecules

F: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• 6.94 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,941	5
Polymers	6,764	2
Non-polymers	177	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_455	x-1/2,y+1/2,z	1

5

G: CC-TypeN-LaUbUcLd

hetero molecules

N: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• 6.97 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,967	5
Polymers	6,764	2
Non-polymers	203	3
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	3_445	x-1/2,y-1/2,z	1

6

H: CC-TypeN-LaUbUcLd

L: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• 6.83 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,826	3
Polymers	6,764	2
Non-polymers	62	1
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	4_545	-x+1/2,y-1/2,-z	1

7

I: CC-TypeN-LaUbUcLd

P: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• 7 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,996	7
Polymers	6,764	2
Non-polymers	232	5
Water	36	2

Symmetry operations:

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

8

J: CC-TypeN-LaUbUcLd

hetero molecules

J: CC-TypeN-LaUbUcLd

hetero molecules

Summary:

• defined by author
• 6.98 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,980	8
Polymers	6,764	2
Non-polymers	216	6
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_756	-x+2,y,-z+1	1

9

M: CC-TypeN-LaUbUcLd

O: CC-TypeN-LaUbUcLd

Summary:

• defined by author
• 6.76 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	6,764	2
Polymers	6,764	2
Non-polymers	0	0
Water	36	2

Symmetry operations:

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

Unit cell

Length a, b, c (Å)	59.891, 133.886, 72.634
Angle α, β, γ (deg.)	90.000, 104.470, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-205- HOH
2	1	B-204- HOH
3	1	B-205- 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	K
1	11	A
2	11	L
1	12	A
2	12	M
1	13	A
2	13	N
1	14	A
2	14	O
1	15	A
2	15	P
1	16	B
2	16	C
1	17	B
2	17	D
1	18	B
2	18	E
1	19	B
2	19	F
1	20	B
2	20	G
1	21	B
2	21	H
1	22	B
2	22	I
1	23	B
2	23	J
1	24	B
2	24	K
1	25	B
2	25	L
1	26	B
2	26	M
1	27	B
2	27	N
1	28	B
2	28	O
1	29	B
2	29	P
1	30	C
2	30	D
1	31	C
2	31	E
1	32	C
2	32	F
1	33	C
2	33	G
1	34	C
2	34	H
1	35	C
2	35	I
1	36	C
2	36	J
1	37	C
2	37	K
1	38	C
2	38	L
1	39	C
2	39	M
1	40	C
2	40	N
1	41	C
2	41	O
1	42	C
2	42	P
1	43	D
2	43	E
1	44	D
2	44	F
1	45	D
2	45	G
1	46	D
2	46	H
1	47	D
2	47	I
1	48	D
2	48	J
1	49	D
2	49	K
1	50	D
2	50	L
1	51	D
2	51	M
1	52	D
2	52	N
1	53	D
2	53	O
1	54	D
2	54	P
1	55	E
2	55	F
1	56	E
2	56	G
1	57	E
2	57	H
1	58	E
2	58	I
1	59	E
2	59	J
1	60	E
2	60	K
1	61	E
2	61	L
1	62	E
2	62	M
1	63	E
2	63	N
1	64	E
2	64	O
1	65	E
2	65	P
1	66	F
2	66	G
1	67	F
2	67	H
1	68	F
2	68	I
1	69	F
2	69	J
1	70	F
2	70	K
1	71	F
2	71	L
1	72	F
2	72	M
1	73	F
2	73	N
1	74	F
2	74	O
1	75	F
2	75	P
1	76	G
2	76	H
1	77	G
2	77	I
1	78	G
2	78	J
1	79	G
2	79	K
1	80	G
2	80	L
1	81	G
2	81	M
1	82	G
2	82	N
1	83	G
2	83	O
1	84	G
2	84	P
1	85	H
2	85	I
1	86	H
2	86	J
1	87	H
2	87	K
1	88	H
2	88	L
1	89	H
2	89	M
1	90	H
2	90	N
1	91	H
2	91	O
1	92	H
2	92	P
1	93	I
2	93	J
1	94	I
2	94	K
1	95	I
2	95	L
1	96	I
2	96	M
1	97	I
2	97	N
1	98	I
2	98	O
1	99	I
2	99	P
1	100	J
2	100	K
1	101	J
2	101	L
1	102	J
2	102	M
1	103	J
2	103	N
1	104	J
2	104	O
1	105	J
2	105	P
1	106	K
2	106	L
1	107	K
2	107	M
1	108	K
2	108	N
1	109	K
2	109	O
1	110	K
2	110	P
1	111	L
2	111	M
1	112	L
2	112	N
1	113	L
2	113	O
1	114	L
2	114	P
1	115	M
2	115	N
1	116	M
2	116	O
1	117	M
2	117	P
1	118	N
2	118	O
1	119	N
2	119	P
1	120	O
2	120	P

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	0	1	0	A	1 - 30
2	0	1	0	B	1 - 30
1	0	2	0	A	1 - 30
2	0	2	0	C	1 - 30
1	0	3	0	A	1 - 30
2	0	3	0	D	1 - 30
1	0	4	0	A	1 - 30
2	0	4	0	E	1 - 30
1	0	5	0	A	1 - 30
2	0	5	0	F	1 - 30
1	0	6	0	A	1 - 30
2	0	6	0	G	1 - 30
1	0	7	0	A	1 - 26
2	0	7	0	H	1 - 26
1	0	8	0	A	1 - 30
2	0	8	0	I	1 - 30
1	0	9	0	A	1 - 30
2	0	9	0	J	1 - 30
1	0	10	0	A	1 - 30
2	0	10	0	K	1 - 30
1	0	11	0	A	1 - 28
2	0	11	0	L	1 - 28
1	0	12	0	A	2 - 19
2	0	12	0	M	2 - 19
1	0	13	0	A	1 - 30
2	0	13	0	N	1 - 30
1	0	14	0	A	3 - 20
2	0	14	0	O	3 - 20
1	0	15	0	A	1 - 30
2	0	15	0	P	1 - 30
1	0	16	0	B	1 - 30
2	0	16	0	C	1 - 30
1	0	17	0	B	1 - 30
2	0	17	0	D	1 - 30
1	0	18	0	B	1 - 30
2	0	18	0	E	1 - 30
1	0	19	0	B	1 - 30
2	0	19	0	F	1 - 30
1	0	20	0	B	1 - 30
2	0	20	0	G	1 - 30
1	0	21	0	B	1 - 26
2	0	21	0	H	1 - 26
1	0	22	0	B	1 - 30
2	0	22	0	I	1 - 30
1	0	23	0	B	1 - 30
2	0	23	0	J	1 - 30
1	0	24	0	B	1 - 30
2	0	24	0	K	1 - 30
1	0	25	0	B	1 - 28
2	0	25	0	L	1 - 28
1	0	26	0	B	2 - 19
2	0	26	0	M	2 - 19
1	0	27	0	B	1 - 30
2	0	27	0	N	1 - 30
1	0	28	0	B	3 - 20
2	0	28	0	O	3 - 20
1	0	29	0	B	1 - 30
2	0	29	0	P	1 - 30
1	0	30	0	C	1 - 30
2	0	30	0	D	1 - 30
1	0	31	0	C	1 - 30
2	0	31	0	E	1 - 30
1	0	32	0	C	1 - 30
2	0	32	0	F	1 - 30
1	0	33	0	C	1 - 30
2	0	33	0	G	1 - 30
1	0	34	0	C	1 - 26
2	0	34	0	H	1 - 26
1	0	35	0	C	1 - 30
2	0	35	0	I	1 - 30
1	0	36	0	C	1 - 30
2	0	36	0	J	1 - 30
1	0	37	0	C	1 - 30
2	0	37	0	K	1 - 30
1	0	38	0	C	1 - 28
2	0	38	0	L	1 - 28
1	0	39	0	C	2 - 19
2	0	39	0	M	2 - 19
1	0	40	0	C	1 - 30
2	0	40	0	N	1 - 30
1	0	41	0	C	3 - 20
2	0	41	0	O	3 - 20
1	0	42	0	C	1 - 30
2	0	42	0	P	1 - 30
1	0	43	0	D	1 - 30
2	0	43	0	E	1 - 30
1	0	44	0	D	1 - 30
2	0	44	0	F	1 - 30
1	0	45	0	D	1 - 30
2	0	45	0	G	1 - 30
1	0	46	0	D	1 - 26
2	0	46	0	H	1 - 26
1	0	47	0	D	1 - 30
2	0	47	0	I	1 - 30
1	0	48	0	D	1 - 30
2	0	48	0	J	1 - 30
1	0	49	0	D	1 - 30
2	0	49	0	K	1 - 30
1	0	50	0	D	1 - 28
2	0	50	0	L	1 - 28
1	0	51	0	D	2 - 19
2	0	51	0	M	2 - 19
1	0	52	0	D	1 - 30
2	0	52	0	N	1 - 30
1	0	53	0	D	3 - 20
2	0	53	0	O	3 - 20
1	0	54	0	D	1 - 30
2	0	54	0	P	1 - 30
1	0	55	0	E	1 - 30
2	0	55	0	F	1 - 30
1	0	56	0	E	1 - 30
2	0	56	0	G	1 - 30
1	0	57	0	E	1 - 26
2	0	57	0	H	1 - 26
1	0	58	0	E	1 - 30
2	0	58	0	I	1 - 30
1	0	59	0	E	1 - 30
2	0	59	0	J	1 - 30
1	0	60	0	E	1 - 30
2	0	60	0	K	1 - 30
1	0	61	0	E	1 - 28
2	0	61	0	L	1 - 28
1	0	62	0	E	2 - 19
2	0	62	0	M	2 - 19
1	0	63	0	E	1 - 30
2	0	63	0	N	1 - 30
1	0	64	0	E	3 - 20
2	0	64	0	O	3 - 20
1	0	65	0	E	1 - 30
2	0	65	0	P	1 - 30
1	0	66	0	F	1 - 30
2	0	66	0	G	1 - 30
1	0	67	0	F	1 - 26
2	0	67	0	H	1 - 26
1	0	68	0	F	1 - 30
2	0	68	0	I	1 - 30
1	0	69	0	F	1 - 30
2	0	69	0	J	1 - 30
1	0	70	0	F	1 - 30
2	0	70	0	K	1 - 30
1	0	71	0	F	1 - 28
2	0	71	0	L	1 - 28
1	0	72	0	F	2 - 19
2	0	72	0	M	2 - 19
1	0	73	0	F	1 - 30
2	0	73	0	N	1 - 30
1	0	74	0	F	3 - 20
2	0	74	0	O	3 - 20
1	0	75	0	F	1 - 30
2	0	75	0	P	1 - 30
1	0	76	0	G	1 - 26
2	0	76	0	H	1 - 26
1	0	77	0	G	1 - 30
2	0	77	0	I	1 - 30
1	0	78	0	G	1 - 30
2	0	78	0	J	1 - 30
1	0	79	0	G	1 - 30
2	0	79	0	K	1 - 30
1	0	80	0	G	1 - 28
2	0	80	0	L	1 - 28
1	0	81	0	G	2 - 19
2	0	81	0	M	2 - 19
1	0	82	0	G	1 - 30
2	0	82	0	N	1 - 30
1	0	83	0	G	3 - 20
2	0	83	0	O	3 - 20
1	0	84	0	G	1 - 30
2	0	84	0	P	1 - 30
1	0	85	0	H	1 - 26
2	0	85	0	I	1 - 26
1	0	86	0	H	1 - 26
2	0	86	0	J	1 - 26
1	0	87	0	H	1 - 26
2	0	87	0	K	1 - 26
1	0	88	0	H	1 - 26
2	0	88	0	L	1 - 26
1	0	89	0	H	2 - 19
2	0	89	0	M	2 - 19
1	0	90	0	H	1 - 26
2	0	90	0	N	1 - 26
1	0	91	0	H	3 - 20
2	0	91	0	O	3 - 20
1	0	92	0	H	1 - 26
2	0	92	0	P	1 - 26
1	0	93	0	I	1 - 30
2	0	93	0	J	1 - 30
1	0	94	0	I	1 - 30
2	0	94	0	K	1 - 30
1	0	95	0	I	1 - 28
2	0	95	0	L	1 - 28
1	0	96	0	I	2 - 19
2	0	96	0	M	2 - 19
1	0	97	0	I	1 - 30
2	0	97	0	N	1 - 30
1	0	98	0	I	3 - 20
2	0	98	0	O	3 - 20
1	0	99	0	I	1 - 30
2	0	99	0	P	1 - 30
1	0	100	0	J	1 - 30
2	0	100	0	K	1 - 30
1	0	101	0	J	1 - 28
2	0	101	0	L	1 - 28
1	0	102	0	J	2 - 19
2	0	102	0	M	2 - 19
1	0	103	0	J	1 - 30
2	0	103	0	N	1 - 30
1	0	104	0	J	3 - 20
2	0	104	0	O	3 - 20
1	0	105	0	J	1 - 30
2	0	105	0	P	1 - 30
1	0	106	0	K	1 - 28
2	0	106	0	L	1 - 28
1	0	107	0	K	2 - 19
2	0	107	0	M	2 - 19
1	0	108	0	K	1 - 30
2	0	108	0	N	1 - 30
1	0	109	0	K	3 - 20
2	0	109	0	O	3 - 20
1	0	110	0	K	1 - 30
2	0	110	0	P	1 - 30
1	0	111	0	L	2 - 19
2	0	111	0	M	2 - 19
1	0	112	0	L	1 - 28
2	0	112	0	N	1 - 28
1	0	113	0	L	3 - 20
2	0	113	0	O	3 - 20
1	0	114	0	L	1 - 28
2	0	114	0	P	1 - 28
1	0	115	0	M	2 - 19
2	0	115	0	N	2 - 19
1	0	116	0	M	3 - 19
2	0	116	0	O	3 - 19
1	0	117	0	M	2 - 19
2	0	117	0	P	2 - 19
1	0	118	0	N	3 - 20
2	0	118	0	O	3 - 20
1	0	119	0	N	1 - 30
2	0	119	0	P	1 - 30
1	0	120	0	O	3 - 20
2	0	120	0	P	3 - 20

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
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120

Components

Protein/peptide , 1 types, 16 molecules A B C D E F G H I J K L M N O P

#1: Protein/peptide

A B C D E F G H I J K L M N O P
CC-TypeN-LaUbUcLd

Details:

Mass: 3382.066 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

Non-polymers , 5 types, 114 molecules

#2: Chemical

A-101 A-102 A-103 B-101 B-102 F-101 J-101 J-102 K-101 K-102 N-101 P-101 P-102
ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Na

#3: Chemical

A-104 C-102 E-102 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL

Details:

Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Chemical

B-103 C-101 C-103 D-101 E-101 G-101 I-101 J-103 L-101 P-103 P-104
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL

Details:

Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₂H₆O₂

#5: Chemical

N-102 ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL

Details:

Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM

#6: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H₂O

Details

• Has ligand of interest: N

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.61 ų/Da / Density % sol: 52.79 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium HEPES 7.5, 70% v/v MPD

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å
• Detector: Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2021
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.979 Å / Relative weight: 1
• Reflection: Resolution: 2.1→48.54 Å / Num. obs: 32270 / % possible obs: 99.93 % / Redundancy: 6.8 % / CC_1/2: 0.988 / CC star: 0.997 / R_merge(I) obs: 0.086 / Net I/σ(I): 10.15
• Reflection shell: Resolution: 2.1→2.175 Å / R_merge(I) obs: 0.4148 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 3196 / CC_1/2: 0.971 / CC star: 0.993

Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
PDB_EXTRACT	3.27	data extraction
xia2		data reduction
Aimless		data scaling
Arcimboldo		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 2.1→48.54 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.934 / SU B: 17.654 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.2607	3227	10 %	RANDOM
Rwork	0.2215	-	-	-
obs	0.2254	29055	99.93 %	-

• 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: 117.92 Ų / B_iso mean: 50.857 Ų / B_iso min: 25.83 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	2.98 Å2	-0 Å2	-0.13 Å2
2-	-	-6.01 Å2	-0 Å2
3-	-	-	2.74 Å2

Refinement step

Cycle: final / Resolution: 2.1→48.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3562	0	89	86	3737
Biso mean	-	-	75.97	69.57	-
Num. residues	-	-	-	-	467

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	3677
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4038
X-RAY DIFFRACTION	r_angle_refined_deg	1.52	1.66	5112
X-RAY DIFFRACTION	r_angle_other_deg	1.149	1.572	9100
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.186	5	450
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.635	25.669	127
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.39	15	690
X-RAY DIFFRACTION	r_chiral_restr	0.088	0.2	311
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3822
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	622

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	823	0.15
1	2	B	823	0.15
2	1	A	828	0.14
2	2	C	828	0.14
3	1	A	811	0.16
3	2	D	811	0.16
4	1	A	827	0.15
4	2	E	827	0.15
5	1	A	843	0.13
5	2	F	843	0.13
6	1	A	814	0.16
6	2	G	814	0.16
7	1	A	717	0.12
7	2	H	717	0.12
8	1	A	820	0.13
8	2	I	820	0.13
9	1	A	827	0.14
9	2	J	827	0.14
10	1	A	811	0.15
10	2	K	811	0.15
11	1	A	759	0.17
11	2	L	759	0.17
12	1	A	458	0.13
12	2	M	458	0.13
13	1	A	815	0.15
13	2	N	815	0.15
14	1	A	459	0.09
14	2	O	459	0.09
15	1	A	820	0.15
15	2	P	820	0.15
16	1	B	847	0.13
16	2	C	847	0.13
17	1	B	827	0.12
17	2	D	827	0.12
18	1	B	839	0.13
18	2	E	839	0.13
19	1	B	840	0.11
19	2	F	840	0.11
20	1	B	836	0.13
20	2	G	836	0.13
21	1	B	732	0.11
21	2	H	732	0.11
22	1	B	820	0.13
22	2	I	820	0.13
23	1	B	830	0.12
23	2	J	830	0.12
24	1	B	827	0.11
24	2	K	827	0.11
25	1	B	768	0.14
25	2	L	768	0.14
26	1	B	472	0.06
26	2	M	472	0.06
27	1	B	837	0.15
27	2	N	837	0.15
28	1	B	462	0.1
28	2	O	462	0.1
29	1	B	824	0.12
29	2	P	824	0.12
30	1	C	830	0.15
30	2	D	830	0.15
31	1	C	836	0.12
31	2	E	836	0.12
32	1	C	847	0.15
32	2	F	847	0.15
33	1	C	834	0.13
33	2	G	834	0.13
34	1	C	734	0.12
34	2	H	734	0.12
35	1	C	827	0.11
35	2	I	827	0.11
36	1	C	829	0.14
36	2	J	829	0.14
37	1	C	826	0.11
37	2	K	826	0.11
38	1	C	766	0.15
38	2	L	766	0.15
39	1	C	473	0.09
39	2	M	473	0.09
40	1	C	843	0.13
40	2	N	843	0.13
41	1	C	461	0.11
41	2	O	461	0.11
42	1	C	829	0.11
42	2	P	829	0.11
43	1	D	836	0.14
43	2	E	836	0.14
44	1	D	819	0.16
44	2	F	819	0.16
45	1	D	848	0.1
45	2	G	848	0.1
46	1	D	724	0.1
46	2	H	724	0.1
47	1	D	808	0.15
47	2	I	808	0.15
48	1	D	825	0.13
48	2	J	825	0.13
49	1	D	823	0.13
49	2	K	823	0.13
50	1	D	771	0.14
50	2	L	771	0.14
51	1	D	464	0.11
51	2	M	464	0.11
52	1	D	813	0.17
52	2	N	813	0.17
53	1	D	455	0.14
53	2	O	455	0.14
54	1	D	828	0.12
54	2	P	828	0.12
55	1	E	842	0.15
55	2	F	842	0.15
56	1	E	851	0.1
56	2	G	851	0.1
57	1	E	720	0.13
57	2	H	720	0.13
58	1	E	828	0.12
58	2	I	828	0.12
59	1	E	851	0.12
59	2	J	851	0.12
60	1	E	845	0.07
60	2	K	845	0.07
61	1	E	783	0.13
61	2	L	783	0.13
62	1	E	472	0.06
62	2	M	472	0.06
63	1	E	824	0.16
63	2	N	824	0.16
64	1	E	459	0.12
64	2	O	459	0.12
65	1	E	853	0.07
65	2	P	853	0.07
66	1	F	828	0.15
66	2	G	828	0.15
67	1	F	722	0.14
67	2	H	722	0.14
68	1	F	838	0.11
68	2	I	838	0.11
69	1	F	844	0.13
69	2	J	844	0.13
70	1	F	831	0.13
70	2	K	831	0.13
71	1	F	768	0.16
71	2	L	768	0.16
72	1	F	470	0.11
72	2	M	470	0.11
73	1	F	838	0.14
73	2	N	838	0.14
74	1	F	463	0.11
74	2	O	463	0.11
75	1	F	837	0.13
75	2	P	837	0.13
76	1	G	732	0.12
76	2	H	732	0.12
77	1	G	832	0.12
77	2	I	832	0.12
78	1	G	847	0.12
78	2	J	847	0.12
79	1	G	850	0.08
79	2	K	850	0.08
80	1	G	792	0.13
80	2	L	792	0.13
81	1	G	475	0.08
81	2	M	475	0.08
82	1	G	829	0.16
82	2	N	829	0.16
83	1	G	468	0.14
83	2	O	468	0.14
84	1	G	852	0.08
84	2	P	852	0.08
85	1	H	727	0.14
85	2	I	727	0.14
86	1	H	737	0.1
86	2	J	737	0.1
87	1	H	737	0.12
87	2	K	737	0.12
88	1	H	733	0.13
88	2	L	733	0.13
89	1	H	483	0.1
89	2	M	483	0.1
90	1	H	728	0.16
90	2	N	728	0.16
91	1	H	474	0.09
91	2	O	474	0.09
92	1	H	722	0.11
92	2	P	722	0.11
93	1	I	837	0.12
93	2	J	837	0.12
94	1	I	847	0.11
94	2	K	847	0.11
95	1	I	785	0.15
95	2	L	785	0.15
96	1	I	477	0.11
96	2	M	477	0.11
97	1	I	831	0.13
97	2	N	831	0.13
98	1	I	477	0.09
98	2	O	477	0.09
99	1	I	832	0.12
99	2	P	832	0.12
100	1	J	844	0.11
100	2	K	844	0.11
101	1	J	787	0.12
101	2	L	787	0.12
102	1	J	482	0.08
102	2	M	482	0.08
103	1	J	834	0.15
103	2	N	834	0.15
104	1	J	474	0.08
104	2	O	474	0.08
105	1	J	856	0.1
105	2	P	856	0.1
106	1	K	788	0.12
106	2	L	788	0.12
107	1	K	473	0.06
107	2	M	473	0.06
108	1	K	810	0.14
108	2	N	810	0.14
109	1	K	460	0.11
109	2	O	460	0.11
110	1	K	837	0.06
110	2	P	837	0.06
111	1	L	472	0.06
111	2	M	472	0.06
112	1	L	757	0.18
112	2	N	757	0.18
113	1	L	457	0.11
113	2	O	457	0.11
114	1	L	776	0.12
114	2	P	776	0.12
115	1	M	458	0.15
115	2	N	458	0.15
116	1	M	408	0.09
116	2	O	408	0.09
117	1	M	466	0.06
117	2	P	466	0.06
118	1	N	470	0.16
118	2	O	470	0.16
119	1	N	844	0.15
119	2	P	844	0.15
120	1	O	455	0.11
120	2	P	455	0.11

LS refinement shell

Resolution: 2.1→2.154 Å / R_factor R_free error: 0

	Rfactor	Num. reflection	% reflection
Rfree	0.378	243	-
Rwork	0.382	2143	-
obs	-	-	99.25 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°2)	L12 (°2)	L13 (°2)	L22 (°2)	L23 (°2)	L33 (°2)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å2)	T12 (Å2)	T13 (Å2)	T22 (Å2)	T23 (Å2)	T33 (Å2)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	9.6479	-9.2684	-3.5396	11.022	3.1955	2.3087	0.3002	0.2252	0.0947	-0.5188	-0.1784	-0.4915	-0.2291	-0.0042	-0.1218	0.0567	-0.0197	0.0561	0.1243	0.0416	0.1274	38.0467	154.9203	46.4639
2	1.2945	0.622	-0.6347	8.8146	2.3101	1.6776	-0.0058	0.0286	-0.0388	-0.0944	-0.0224	0.1236	-0.037	0.0413	0.0282	0.118	0.0049	-0.0369	0.1356	0.0198	0.066	33.4967	114.168	-1.6109
3	1.7004	2.1145	-1.091	8.7149	-3.0789	2.0352	-0.0387	-0.0246	-0.0286	-0.0104	0.0755	0.3878	0.0859	-0.097	-0.0368	0.1044	-0.0325	-0.0128	0.168	-0.0451	0.1032	39.5247	110.1432	31.3092
4	4.1394	4.216	-0.7178	6.182	-1.7065	1.0311	0.0257	0.0006	-0.0076	0.0753	-0.0183	0.1062	0.0131	0.0053	-0.0073	0.1423	-0.0021	0.0333	0.1349	-0.0572	0.1237	40.7927	105.9211	24.8252
5	11.1227	-8.9502	5.5985	14.3132	-5.6421	3.791	0.0878	-0.0026	0.0252	-0.1125	0.0563	0.2605	0.2817	-0.0238	-0.1441	0.2979	0.0889	0.032	0.1722	-0.0256	0.0692	17.2339	135.5303	9.1698
6	1.824	-2.2384	1.293	8.622	-2.6949	1.3074	0.0039	0.0562	-0.0462	0.0691	0.1531	0.3064	-0.0796	-0.0871	-0.1569	0.1878	0.0687	0.0538	0.2093	-0.0032	0.0988	47.663	64.928	2.5002
7	1.6448	1.2291	0.6269	10.6376	2.9501	1.6144	-0.0233	-0.0401	0.017	-0.2763	0.1527	-0.1646	-0.2046	0.1379	-0.1294	0.0778	-0.0055	0.0354	0.1706	0.021	0.0669	33.2579	68.9344	34.6514
8	6.8671	6.7826	1.913	13.3098	2.6949	4.0108	-0.0468	-0.1362	0.3943	0.2785	-0.1618	0.7615	0.3453	-0.2823	0.2087	0.1064	-0.0179	0.0605	0.1182	0.0019	0.0723	15.2703	80.7442	-12.0759
9	4.5551	-4.6897	-2.0478	7.7777	2.7205	1.8565	0.0221	-0.0091	0.0114	-0.1065	-0.0319	-0.1318	-0.1137	0.008	0.0099	0.129	-0.0076	-0.0198	0.1696	0.018	0.0734	42.8101	103.6933	9.0173
10	1.331	0.3747	-0.3662	10.5624	2.0684	1.3959	-0.0794	-0.0197	-0.0692	0.0555	0.0703	0.132	0.1159	0.013	0.0091	0.0744	0.0181	-0.0068	0.138	0.0271	0.0685	54.7147	118.1052	35.5961
11	9.1056	6.9778	3.258	8.3076	2.1573	4.3907	-0.1029	-0.1865	0.208	-0.1317	-0.0938	0.2399	-0.1275	0.095	0.1968	0.0584	0.0289	0.033	0.0748	0.0239	0.0442	37.8771	81.1756	24.3213
12	12.8175	-9.569	-4.2406	11.8429	4.2439	5.1604	-0.2919	0.0235	-0.4465	0.1139	-0.0123	-0.3364	0.3901	0.2498	0.3042	0.1137	0.0144	0.057	0.0863	0.0414	0.1451	19.5204	152.9048	9.7268
13	6.2513	2.5569	4.3717	2.479	3.9908	7.6514	0.0634	0.0728	-0.2562	-0.1865	0.0719	0.0217	-0.0821	-0.1218	-0.1353	0.1966	0.007	0.0044	0.2715	-0.0026	0.207	65.768	128.84	15.6512
14	9.0344	6.412	3.9831	11.3787	3.8562	4.8831	0.2028	-0.2975	-0.0187	0.1478	-0.1628	-0.2869	0.0437	0.1626	-0.04	0.0148	0.0012	0.0121	0.1334	0.0294	0.0305	66.8441	137.75	28.284
15	0.8484	1.0425	1.2376	1.7306	1.5144	6.6048	-0.0491	0.1527	-0.1148	0.0047	0.0846	0.0751	-0.0486	0.2078	-0.0355	0.23	0.0124	0.0003	0.3303	-0.0352	0.2621	69.4625	120.6808	14.9733
16	1.5932	-0.8397	-0.3741	7.3003	3.0285	2.1144	-0.0538	0.0024	0.0074	-0.022	0.0561	-0.2025	0.0625	0.126	-0.0023	0.1477	0.0163	-0.0186	0.1641	0.0122	0.0842	41.4362	105.9253	1.7641

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 31
2	X-RAY DIFFRACTION	2	B	0 - 30
3	X-RAY DIFFRACTION	3	C	0 - 30
4	X-RAY DIFFRACTION	4	D	0 - 30
5	X-RAY DIFFRACTION	5	E	0 - 101
6	X-RAY DIFFRACTION	6	F	0 - 30
7	X-RAY DIFFRACTION	7	G	0 - 30
8	X-RAY DIFFRACTION	8	H	0 - 27
9	X-RAY DIFFRACTION	9	I	0 - 30
10	X-RAY DIFFRACTION	10	J	0 - 30
11	X-RAY DIFFRACTION	11	K	0 - 30
12	X-RAY DIFFRACTION	12	L	0 - 29
13	X-RAY DIFFRACTION	13	M	2 - 20
14	X-RAY DIFFRACTION	14	N	0 - 30
15	X-RAY DIFFRACTION	15	O	3 - 21
16	X-RAY DIFFRACTION	16	P	0 - 30