PDB-6rlm: Crystal structure of AT1412dm Fab fragment

Basic information

• Entry: Database: PDB / ID: 6rlm
• Title: Crystal structure of AT1412dm Fab fragment

Components

• AT1412dm Fab (Heavy Chain)
• AT1412dm Fab (Light Chain)

• Keywords: IMMUNE SYSTEM / Antibody / Fab / CD9-binding / affinity-improvement
• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
• Authors: Neviani, V. / Pearce, N.M. / Pos, W. / Schotte, R. / Spits, H. / Gros, P.

Funding support

Netherlands, 1items

Organization	Grant number	Country
Netherlands Organisation for Scientific Research	024.002.009	Netherlands

• Citation: Journal: To Be Published; Title: Structural basis of a homo-dimerization site in tetraspanin CD9 targeted by a melanoma patient-derived antibody; Authors: Neviani, V. / Pos, W. / Schotte, R. / Wagner, K. / Go, D.M. / Fatmawati, C. / Kedde, M. / Claassen, Y.B. / Kroon-Batenburg, L. / Lutz, M. / Verdegaal, E.M.E. / van der Burg, S.H. / Spits, H. / Gros, P.

History

Deposition	May 2, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 12, 2021	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 / struct_ncs_dom_lim Item: _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
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Assembly

Deposited unit

A: AT1412dm Fab (Heavy Chain)

B: AT1412dm Fab (Light Chain)

C: AT1412dm Fab (Heavy Chain)

D: AT1412dm Fab (Light Chain)

E: AT1412dm Fab (Heavy Chain)

F: AT1412dm Fab (Light Chain)

G: AT1412dm Fab (Heavy Chain)

H: AT1412dm Fab (Light Chain)

I: AT1412dm Fab (Heavy Chain)

J: AT1412dm Fab (Light Chain)

K: AT1412dm Fab (Heavy Chain)

L: AT1412dm Fab (Light Chain)

M: AT1412dm Fab (Heavy Chain)

N: AT1412dm Fab (Light Chain)

O: AT1412dm Fab (Heavy Chain)

P: AT1412dm Fab (Light Chain)

hetero molecules

Summary:

• 389 kDa, 16 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	388,502	20
Polymers	388,360	16
Non-polymers	142	4
Water	0	0

1

A: AT1412dm Fab (Heavy Chain)

B: AT1412dm Fab (Light Chain)

Summary:

• defined by author&software
• 48.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,545	2
Polymers	48,545	2
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3410 Å2
ΔGint	-26 kcal/mol
Surface area	19970 Å2
Method	PISA

2

C: AT1412dm Fab (Heavy Chain)

D: AT1412dm Fab (Light Chain)

hetero molecules

Summary:

• defined by author&software
• 48.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,580	3
Polymers	48,545	2
Non-polymers	35	1
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3530 Å2
ΔGint	-39 kcal/mol
Surface area	19960 Å2
Method	PISA

3

E: AT1412dm Fab (Heavy Chain)

F: AT1412dm Fab (Light Chain)

Summary:

• defined by author&software
• 48.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,545	2
Polymers	48,545	2
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3920 Å2
ΔGint	-28 kcal/mol
Surface area	19650 Å2
Method	PISA

4

G: AT1412dm Fab (Heavy Chain)

H: AT1412dm Fab (Light Chain)

hetero molecules

Summary:

• defined by author&software
• 48.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,580	3
Polymers	48,545	2
Non-polymers	35	1
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3540 Å2
ΔGint	-39 kcal/mol
Surface area	19660 Å2
Method	PISA

5

I: AT1412dm Fab (Heavy Chain)

J: AT1412dm Fab (Light Chain)

hetero molecules

Summary:

• defined by author&software
• 48.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,580	3
Polymers	48,545	2
Non-polymers	35	1
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3950 Å2
ΔGint	-39 kcal/mol
Surface area	19790 Å2
Method	PISA

6

K: AT1412dm Fab (Heavy Chain)

L: AT1412dm Fab (Light Chain)

hetero molecules

Summary:

• defined by author&software
• 48.6 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,580	3
Polymers	48,545	2
Non-polymers	35	1
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3590 Å2
ΔGint	-39 kcal/mol
Surface area	19630 Å2
Method	PISA

7

M: AT1412dm Fab (Heavy Chain)

N: AT1412dm Fab (Light Chain)

Summary:

• defined by author&software
• 48.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,545	2
Polymers	48,545	2
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3560 Å2
ΔGint	-25 kcal/mol
Surface area	19830 Å2
Method	PISA

8

O: AT1412dm Fab (Heavy Chain)

P: AT1412dm Fab (Light Chain)

Summary:

• defined by author&software
• 48.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	48,545	2
Polymers	48,545	2
Non-polymers	0	0
Water	0

Symmetry operations:

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

Calculated values:

Buried area	3320 Å2
ΔGint	-26 kcal/mol
Surface area	19630 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	224.909, 238.594, 209.812
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C2221

Noncrystallographic symmetry (NCS)

NCS domain:

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

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	VAL	VAL	LYS	LYS	A	A	2 - 229	2 - 221
2	1	VAL	VAL	LYS	LYS	C	C	2 - 229	2 - 221
1	2	VAL	VAL	LYS	LYS	A	A	2 - 229	2 - 221
2	2	VAL	VAL	LYS	LYS	E	E	2 - 229	2 - 221
1	3	VAL	VAL	PRO	PRO	A	A	2 - 228	2 - 220
2	3	VAL	VAL	PRO	PRO	G	G	2 - 228	2 - 220
1	4	VAL	VAL	LYS	LYS	A	A	2 - 229	2 - 221
2	4	VAL	VAL	LYS	LYS	I	I	2 - 229	2 - 221
1	5	VAL	VAL	PRO	PRO	A	A	2 - 228	2 - 220
2	5	VAL	VAL	PRO	PRO	K	K	2 - 228	2 - 220
1	6	VAL	VAL	LYS	LYS	A	A	2 - 229	2 - 221
2	6	VAL	VAL	LYS	LYS	M	M	2 - 229	2 - 221
1	7	VAL	VAL	PRO	PRO	A	A	2 - 228	2 - 220
2	7	VAL	VAL	PRO	PRO	O	O	2 - 228	2 - 220
1	8	ILE	ILE	GLY	GLY	B	B	2 - 228	2 - 218
2	8	ILE	ILE	GLY	GLY	D	D	2 - 228	2 - 218
1	9	ASP	ASP	GLU	GLU	B	B	1 - 229	1 - 219
2	9	ASP	ASP	GLU	GLU	F	F	1 - 229	1 - 219
1	10	ILE	ILE	GLY	GLY	B	B	2 - 228	2 - 218
2	10	ILE	ILE	GLY	GLY	H	H	2 - 228	2 - 218
1	11	ASP	ASP	GLU	GLU	B	B	1 - 229	1 - 219
2	11	ASP	ASP	GLU	GLU	J	J	1 - 229	1 - 219
1	12	ASP	ASP	GLU	GLU	B	B	1 - 229	1 - 219
2	12	ASP	ASP	GLU	GLU	L	L	1 - 229	1 - 219
1	13	ASP	ASP	GLU	GLU	B	B	1 - 229	1 - 219
2	13	ASP	ASP	GLU	GLU	N	N	1 - 229	1 - 219
1	14	ASP	ASP	GLU	GLU	B	B	1 - 229	1 - 219
2	14	ASP	ASP	GLU	GLU	P	P	1 - 229	1 - 219
1	15	VAL	VAL	LYS	LYS	C	C	2 - 229	2 - 221
2	15	VAL	VAL	LYS	LYS	E	E	2 - 229	2 - 221
1	16	VAL	VAL	GLU	GLU	C	C	2 - 227	2 - 219
2	16	VAL	VAL	GLU	GLU	G	G	2 - 227	2 - 219
1	17	VAL	VAL	LYS	LYS	C	C	2 - 229	2 - 221
2	17	VAL	VAL	LYS	LYS	I	I	2 - 229	2 - 221
1	18	VAL	VAL	PRO	PRO	C	C	2 - 228	2 - 220
2	18	VAL	VAL	PRO	PRO	K	K	2 - 228	2 - 220
1	19	VAL	VAL	LYS	LYS	C	C	2 - 229	2 - 221
2	19	VAL	VAL	LYS	LYS	M	M	2 - 229	2 - 221
1	20	VAL	VAL	PRO	PRO	C	C	2 - 228	2 - 220
2	20	VAL	VAL	PRO	PRO	O	O	2 - 228	2 - 220
1	21	ILE	ILE	GLY	GLY	D	D	2 - 228	2 - 218
2	21	ILE	ILE	GLY	GLY	F	F	2 - 228	2 - 218
1	22	ILE	ILE	GLU	GLU	D	D	2 - 229	2 - 219
2	22	ILE	ILE	GLU	GLU	H	H	2 - 229	2 - 219
1	23	ILE	ILE	GLY	GLY	D	D	2 - 228	2 - 218
2	23	ILE	ILE	GLY	GLY	J	J	2 - 228	2 - 218
1	24	ILE	ILE	GLY	GLY	D	D	2 - 228	2 - 218
2	24	ILE	ILE	GLY	GLY	L	L	2 - 228	2 - 218
1	25	ILE	ILE	GLY	GLY	D	D	2 - 228	2 - 218
2	25	ILE	ILE	GLY	GLY	N	N	2 - 228	2 - 218
1	26	ILE	ILE	GLY	GLY	D	D	2 - 228	2 - 218
2	26	ILE	ILE	GLY	GLY	P	P	2 - 228	2 - 218
1	27	VAL	VAL	PRO	PRO	E	E	2 - 228	2 - 220
2	27	VAL	VAL	PRO	PRO	G	G	2 - 228	2 - 220
1	28	VAL	VAL	PRO	PRO	E	E	2 - 228	2 - 220
2	28	VAL	VAL	PRO	PRO	I	I	2 - 228	2 - 220
1	29	VAL	VAL	PRO	PRO	E	E	2 - 228	2 - 220
2	29	VAL	VAL	PRO	PRO	K	K	2 - 228	2 - 220
1	30	VAL	VAL	LYS	LYS	E	E	2 - 229	2 - 221
2	30	VAL	VAL	LYS	LYS	M	M	2 - 229	2 - 221
1	31	VAL	VAL	PRO	PRO	E	E	2 - 228	2 - 220
2	31	VAL	VAL	PRO	PRO	O	O	2 - 228	2 - 220
1	32	ILE	ILE	GLY	GLY	F	F	2 - 228	2 - 218
2	32	ILE	ILE	GLY	GLY	H	H	2 - 228	2 - 218
1	33	ASP	ASP	GLU	GLU	F	F	1 - 229	1 - 219
2	33	ASP	ASP	GLU	GLU	J	J	1 - 229	1 - 219
1	34	ASP	ASP	GLU	GLU	F	F	1 - 229	1 - 219
2	34	ASP	ASP	GLU	GLU	L	L	1 - 229	1 - 219
1	35	ASP	ASP	GLU	GLU	F	F	1 - 229	1 - 219
2	35	ASP	ASP	GLU	GLU	N	N	1 - 229	1 - 219
1	36	ASP	ASP	GLU	GLU	F	F	1 - 229	1 - 219
2	36	ASP	ASP	GLU	GLU	P	P	1 - 229	1 - 219
1	37	VAL	VAL	PRO	PRO	G	G	2 - 228	2 - 220
2	37	VAL	VAL	PRO	PRO	I	I	2 - 228	2 - 220
1	38	VAL	VAL	PRO	PRO	G	G	2 - 228	2 - 220
2	38	VAL	VAL	PRO	PRO	K	K	2 - 228	2 - 220
1	39	VAL	VAL	PRO	PRO	G	G	2 - 228	2 - 220
2	39	VAL	VAL	PRO	PRO	M	M	2 - 228	2 - 220
1	40	VAL	VAL	PRO	PRO	G	G	2 - 228	2 - 220
2	40	VAL	VAL	PRO	PRO	O	O	2 - 228	2 - 220
1	41	ILE	ILE	GLY	GLY	H	H	2 - 228	2 - 218
2	41	ILE	ILE	GLY	GLY	J	J	2 - 228	2 - 218
1	42	ILE	ILE	GLY	GLY	H	H	2 - 228	2 - 218
2	42	ILE	ILE	GLY	GLY	L	L	2 - 228	2 - 218
1	43	ILE	ILE	GLY	GLY	H	H	2 - 228	2 - 218
2	43	ILE	ILE	GLY	GLY	N	N	2 - 228	2 - 218
1	44	ILE	ILE	GLY	GLY	H	H	2 - 228	2 - 218
2	44	ILE	ILE	GLY	GLY	P	P	2 - 228	2 - 218
1	45	VAL	VAL	PRO	PRO	I	I	2 - 228	2 - 220
2	45	VAL	VAL	PRO	PRO	K	K	2 - 228	2 - 220
1	46	VAL	VAL	LYS	LYS	I	I	2 - 229	2 - 221
2	46	VAL	VAL	LYS	LYS	M	M	2 - 229	2 - 221
1	47	VAL	VAL	PRO	PRO	I	I	2 - 228	2 - 220
2	47	VAL	VAL	PRO	PRO	O	O	2 - 228	2 - 220
1	48	ASP	ASP	GLU	GLU	J	J	1 - 229	1 - 219
2	48	ASP	ASP	GLU	GLU	L	L	1 - 229	1 - 219
1	49	ASP	ASP	GLU	GLU	J	J	1 - 229	1 - 219
2	49	ASP	ASP	GLU	GLU	N	N	1 - 229	1 - 219
1	50	ASP	ASP	GLU	GLU	J	J	1 - 229	1 - 219
2	50	ASP	ASP	GLU	GLU	P	P	1 - 229	1 - 219
1	51	VAL	VAL	PRO	PRO	K	K	2 - 228	2 - 220
2	51	VAL	VAL	PRO	PRO	M	M	2 - 228	2 - 220
1	52	VAL	VAL	PRO	PRO	K	K	2 - 228	2 - 220
2	52	VAL	VAL	PRO	PRO	O	O	2 - 228	2 - 220
1	53	ASP	ASP	GLU	GLU	L	L	1 - 229	1 - 219
2	53	ASP	ASP	GLU	GLU	N	N	1 - 229	1 - 219
1	54	ASP	ASP	GLU	GLU	L	L	1 - 229	1 - 219
2	54	ASP	ASP	GLU	GLU	P	P	1 - 229	1 - 219
1	55	VAL	VAL	PRO	PRO	M	M	2 - 228	2 - 220
2	55	VAL	VAL	PRO	PRO	O	O	2 - 228	2 - 220
1	56	ASP	ASP	GLU	GLU	N	N	1 - 229	1 - 219
2	56	ASP	ASP	GLU	GLU	P	P	1 - 229	1 - 219

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

Components

#1: Antibody

A C E G I K M O
AT1412dm Fab (Heavy Chain)

Details:

Mass: 24311.205 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

#2: Antibody

B D F H J L N P
AT1412dm Fab (Light Chain)

Details:

Mass: 24233.760 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

#3: Chemical

C-301 G-301 J-301 K-301
ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

• Has protein modification: Y

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 3.74 ų/Da / Density % sol: 67.07 %
• Crystal grow: Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 400, potassium chloride, TRIS

Data collection

• Diffraction: Mean temperature: 100 K / Serial crystal experiment: N
• Diffraction source: Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
• Detector: Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2017
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.97 Å / Relative weight: 1
• Reflection: Resolution: 2.5→163.66 Å / Num. obs: 192872 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC_1/2: 0.845 / R_merge(I) obs: 0.143 / R_pim(I) all: 0.061 / R_rim(I) all: 0.156 / Net I/σ(I): 7 / Num. measured all: 1251551 / Scaling rejects: 1277

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. measured all	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	Net I/σ(I) obs	% possible all
2.5-2.54	4.6	3.138	41700	9123	0.23	1.594	3.538	0.5	96.1
13.69-163.66	6	0.057	7907	1315	0.587	0.037	0.069	23.2	100

Processing

Software

Name	Version	Classification
DIALS		data reduction
Aimless	0.6.3	data scaling
PHASER		phasing
Coot		model building
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.25	data extraction

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I1D

5i1d

Resolution: 2.5→163.66 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.937 / SU B: 18.633 / SU ML: 0.339 / SU R Cruickshank DPI: 0.3634 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.363 / ESU R Free: 0.259
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.267	9439	4.9 %	RANDOM
Rwork	0.2423	-	-	-
obs	0.2436	182773	99.4 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 178.84 Ų / B_iso mean: 73.815 Ų / B_iso min: 37.19 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-4.47 Å2	0 Å2	0 Å2
2-	-	-3 Å2	0 Å2
3-	-	-	7.47 Å2

Refinement step

Cycle: final / Resolution: 2.5→163.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26540	0	4	0	26544
Biso mean	-	-	78.93	-	-
Num. residues	-	-	-	-	3466

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	27212
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	24152
X-RAY DIFFRACTION	r_angle_refined_deg	1.482	1.641	37054
X-RAY DIFFRACTION	r_angle_other_deg	1.178	1.57	56345
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.849	5	3442
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.079	22.924	1221
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.783	15	4263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.512	15	112
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	3540
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	30538
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5674

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	6284	0.05
1	2	C	6284	0.05
2	1	A	6281	0.06
2	2	E	6281	0.06
3	1	A	6251	0.06
3	2	G	6251	0.06
4	1	A	6274	0.06
4	2	I	6274	0.06
5	1	A	6216	0.05
5	2	K	6216	0.05
6	1	A	6278	0.06
6	2	M	6278	0.06
7	1	A	6019	0.06
7	2	O	6019	0.06
8	1	B	6525	0.05
8	2	D	6525	0.05
9	1	B	6676	0.04
9	2	F	6676	0.04
10	1	B	6602	0.04
10	2	H	6602	0.04
11	1	B	6621	0.05
11	2	J	6621	0.05
12	1	B	6667	0.04
12	2	L	6667	0.04
13	1	B	6617	0.05
13	2	N	6617	0.05
14	1	B	6612	0.05
14	2	P	6612	0.05
15	1	C	6252	0.05
15	2	E	6252	0.05
16	1	C	6240	0.05
16	2	G	6240	0.05
17	1	C	6260	0.06
17	2	I	6260	0.06
18	1	C	6191	0.05
18	2	K	6191	0.05
19	1	C	6263	0.05
19	2	M	6263	0.05
20	1	C	6029	0.06
20	2	O	6029	0.06
21	1	D	6568	0.05
21	2	F	6568	0.05
22	1	D	6603	0.04
22	2	H	6603	0.04
23	1	D	6599	0.04
23	2	J	6599	0.04
24	1	D	6552	0.06
24	2	L	6552	0.06
25	1	D	6590	0.05
25	2	N	6590	0.05
26	1	D	6548	0.06
26	2	P	6548	0.06
27	1	E	6221	0.06
27	2	G	6221	0.06
28	1	E	6366	0.07
28	2	I	6366	0.07
29	1	E	6192	0.06
29	2	K	6192	0.06
30	1	E	6249	0.06
30	2	M	6249	0.06
31	1	E	6040	0.06
31	2	O	6040	0.06
32	1	F	6513	0.05
32	2	H	6513	0.05
33	1	F	6692	0.04
33	2	J	6692	0.04
34	1	F	6743	0.04
34	2	L	6743	0.04
35	1	F	6669	0.04
35	2	N	6669	0.04
36	1	F	6587	0.06
36	2	P	6587	0.06
37	1	G	6230	0.05
37	2	I	6230	0.05
38	1	G	6236	0.05
38	2	K	6236	0.05
39	1	G	6210	0.06
39	2	M	6210	0.06
40	1	G	6038	0.06
40	2	O	6038	0.06
41	1	H	6529	0.05
41	2	J	6529	0.05
42	1	H	6522	0.06
42	2	L	6522	0.06
43	1	H	6536	0.05
43	2	N	6536	0.05
44	1	H	6535	0.05
44	2	P	6535	0.05
45	1	I	6175	0.07
45	2	K	6175	0.07
46	1	I	6297	0.05
46	2	M	6297	0.05
47	1	I	6001	0.07
47	2	O	6001	0.07
48	1	J	6696	0.04
48	2	L	6696	0.04
49	1	J	6698	0.03
49	2	N	6698	0.03
50	1	J	6621	0.05
50	2	P	6621	0.05
51	1	K	6154	0.07
51	2	M	6154	0.07
52	1	K	6029	0.06
52	2	O	6029	0.06
53	1	L	6664	0.04
53	2	N	6664	0.04
54	1	L	6599	0.06
54	2	P	6599	0.06
55	1	M	6011	0.07
55	2	O	6011	0.07
56	1	N	6638	0.05
56	2	P	6638	0.05

LS refinement shell

Resolution: 2.5→2.565 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.441	639	-
Rwork	0.453	12919	-
all	-	13558	-
obs	-	-	95.55 %