PDB-8qmd: Human NK cell receptor NKp80, extracellular domain

ID or keywords:

Entry

Database: PDB / ID: 8qmd

Title

Human NK cell receptor NKp80, extracellular domain

Components

Killer cell lectin-like receptor subfamily F member 1

Keywords

IMMUNE SYSTEM / NK cell receptor / NKp80 / C-type lectin-like

Function / homology

Function and homology information

NK T cell activation / MHC class I receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / carbohydrate binding / cell surface receptor signaling pathway / innate immune response / membrane / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Blaha, J. / Pazderova, K. / Kalouskova, B. / Wilmanns, M. / Vanek, O.

Funding support

Czech Republic, European Union, 3items

Citation

Journal: To Be Published
Title: Structure of the human NK cell activation receptor NKp80 ectodomain
Authors: Pazderova, K. / Kalouskova, B. / Blaha, J. / Wilmanns, M. / Vanek, O.

History

Deposition	Sep 22, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qmd.cif.gz	699.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8qmd.ent.gz	448.6 KB	Display	PDB format
PDBx/mmJSON format	8qmd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qm/8qmd ftp://data.pdbj.org/pub/pdb/validation_reports/qm/8qmd	HTTPS FTP

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Related structure data

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	#232 - Apr 2019 Proteins and Biominerals similarity (6) #134 - Feb 2011 Integrin similarity (6) #75 - Mar 2006 Tissue Factor similarity (6) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

C: Killer cell lectin-like receptor subfamily F member 1

D: Killer cell lectin-like receptor subfamily F member 1

A: Killer cell lectin-like receptor subfamily F member 1

B: Killer cell lectin-like receptor subfamily F member 1

E: Killer cell lectin-like receptor subfamily F member 1

F: Killer cell lectin-like receptor subfamily F member 1

G: Killer cell lectin-like receptor subfamily F member 1

H: Killer cell lectin-like receptor subfamily F member 1

I: Killer cell lectin-like receptor subfamily F member 1

J: Killer cell lectin-like receptor subfamily F member 1

hetero molecules

213 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Killer cell lectin-like receptor subfamily F member 1

D: Killer cell lectin-like receptor subfamily F member 1

hetero molecules

defined by author
Evidence: equilibrium centrifugation, Analytical ultracentrifugation - sedimentation velocity experiment shows homodimer formation at high protein concentration
42.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Killer cell lectin-like receptor subfamily F member 1

B: Killer cell lectin-like receptor subfamily F member 1

hetero molecules

defined by author
42.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Killer cell lectin-like receptor subfamily F member 1

F: Killer cell lectin-like receptor subfamily F member 1

hetero molecules

defined by author
42.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Killer cell lectin-like receptor subfamily F member 1

H: Killer cell lectin-like receptor subfamily F member 1

hetero molecules

defined by author
42.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Killer cell lectin-like receptor subfamily F member 1

J: Killer cell lectin-like receptor subfamily F member 1

hetero molecules

defined by author
42.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	183.544, 183.544, 123.668
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Auth asym-ID: C / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	TYR	TYR	51 - 171	51 - 171
2	1	1	THR	THR	TYR	TYR	51 - 171	51 - 171
3	2	2	THR	THR	THR	THR	51 - 173	51 - 173
4	2	2	THR	THR	THR	THR	51 - 173	51 - 173
5	3	3	THR	THR	GLY	GLY	51 - 172	51 - 172
6	3	3	THR	THR	GLY	GLY	51 - 172	51 - 172
7	4	4	THR	THR	GLY	GLY	51 - 172	51 - 172
8	4	4	THR	THR	GLY	GLY	51 - 172	51 - 172
9	5	5	THR	THR	GLY	GLY	51 - 172	51 - 172
10	5	5	THR	THR	GLY	GLY	51 - 172	51 - 172
11	6	6	LEU	LEU	GLY	GLY	53 - 172	53 - 172
12	6	6	LEU	LEU	GLY	GLY	53 - 172	53 - 172
13	7	7	THR	THR	THR	THR	51 - 173	51 - 173
14	7	7	THR	THR	THR	THR	51 - 173	51 - 173
15	8	8	THR	THR	THR	THR	51 - 173	51 - 173
16	8	8	THR	THR	THR	THR	51 - 173	51 - 173
17	9	9	VAL	VAL	GLY	GLY	52 - 172	52 - 172
18	9	9	VAL	VAL	GLY	GLY	52 - 172	52 - 172
19	10	10	THR	THR	TYR	TYR	51 - 171	51 - 171
20	10	10	THR	THR	TYR	TYR	51 - 171	51 - 171
21	11	11	THR	THR	TYR	TYR	51 - 171	51 - 171
22	11	11	THR	THR	TYR	TYR	51 - 171	51 - 171
23	12	12	THR	THR	TYR	TYR	51 - 171	51 - 171
24	12	12	THR	THR	TYR	TYR	51 - 171	51 - 171
25	13	13	THR	THR	TYR	TYR	51 - 171	51 - 171
26	13	13	THR	THR	TYR	TYR	51 - 171	51 - 171
27	14	14	LEU	LEU	TYR	TYR	53 - 171	53 - 171
28	14	14	LEU	LEU	TYR	TYR	53 - 171	53 - 171
29	15	15	THR	THR	TYR	TYR	51 - 171	51 - 171
30	15	15	THR	THR	TYR	TYR	51 - 171	51 - 171
31	16	16	THR	THR	TYR	TYR	51 - 171	51 - 171
32	16	16	THR	THR	TYR	TYR	51 - 171	51 - 171
33	17	17	VAL	VAL	TYR	TYR	52 - 171	52 - 171
34	17	17	VAL	VAL	TYR	TYR	52 - 171	52 - 171
35	18	18	THR	THR	GLY	GLY	51 - 172	51 - 172
36	18	18	THR	THR	GLY	GLY	51 - 172	51 - 172
37	19	19	THR	THR	GLY	GLY	51 - 172	51 - 172
38	19	19	THR	THR	GLY	GLY	51 - 172	51 - 172
39	20	20	THR	THR	GLY	GLY	51 - 172	51 - 172
40	20	20	THR	THR	GLY	GLY	51 - 172	51 - 172
41	21	21	LEU	LEU	GLY	GLY	53 - 172	53 - 172
42	21	21	LEU	LEU	GLY	GLY	53 - 172	53 - 172
43	22	22	THR	THR	THR	THR	51 - 173	51 - 173
44	22	22	THR	THR	THR	THR	51 - 173	51 - 173
45	23	23	THR	THR	THR	THR	51 - 173	51 - 173
46	23	23	THR	THR	THR	THR	51 - 173	51 - 173
47	24	24	VAL	VAL	GLY	GLY	52 - 172	52 - 172
48	24	24	VAL	VAL	GLY	GLY	52 - 172	52 - 172
49	25	25	THR	THR	THR	THR	51 - 173	51 - 173
50	25	25	THR	THR	THR	THR	51 - 173	51 - 173
51	26	26	THR	THR	THR	THR	51 - 173	51 - 173
52	26	26	THR	THR	THR	THR	51 - 173	51 - 173
53	27	27	LEU	LEU	GLY	GLY	53 - 172	53 - 172
54	27	27	LEU	LEU	GLY	GLY	53 - 172	53 - 172
55	28	28	THR	THR	GLY	GLY	51 - 172	51 - 172
56	28	28	THR	THR	GLY	GLY	51 - 172	51 - 172
57	29	29	THR	THR	GLY	GLY	51 - 172	51 - 172
58	29	29	THR	THR	GLY	GLY	51 - 172	51 - 172
59	30	30	VAL	VAL	GLY	GLY	52 - 172	52 - 172
60	30	30	VAL	VAL	GLY	GLY	52 - 172	52 - 172
61	31	31	THR	THR	THR	THR	51 - 173	51 - 173
62	31	31	THR	THR	THR	THR	51 - 173	51 - 173
63	32	32	LEU	LEU	GLY	GLY	53 - 172	53 - 172
64	32	32	LEU	LEU	GLY	GLY	53 - 172	53 - 172
65	33	33	THR	THR	GLY	GLY	51 - 172	51 - 172
66	33	33	THR	THR	GLY	GLY	51 - 172	51 - 172
67	34	34	THR	THR	GLY	GLY	51 - 172	51 - 172
68	34	34	THR	THR	GLY	GLY	51 - 172	51 - 172
69	35	35	VAL	VAL	GLY	GLY	52 - 172	52 - 172
70	35	35	VAL	VAL	GLY	GLY	52 - 172	52 - 172
71	36	36	LEU	LEU	GLY	GLY	53 - 172	53 - 172
72	36	36	LEU	LEU	GLY	GLY	53 - 172	53 - 172
73	37	37	THR	THR	GLY	GLY	51 - 172	51 - 172
74	37	37	THR	THR	GLY	GLY	51 - 172	51 - 172
75	38	38	THR	THR	GLY	GLY	51 - 172	51 - 172
76	38	38	THR	THR	GLY	GLY	51 - 172	51 - 172
77	39	39	VAL	VAL	GLY	GLY	52 - 172	52 - 172
78	39	39	VAL	VAL	GLY	GLY	52 - 172	52 - 172
79	40	40	LEU	LEU	GLY	GLY	53 - 172	53 - 172
80	40	40	LEU	LEU	GLY	GLY	53 - 172	53 - 172
81	41	41	LEU	LEU	GLY	GLY	53 - 172	53 - 172
82	41	41	LEU	LEU	GLY	GLY	53 - 172	53 - 172
83	42	42	LEU	LEU	GLY	GLY	53 - 172	53 - 172
84	42	42	LEU	LEU	GLY	GLY	53 - 172	53 - 172
85	43	43	THR	THR	THR	THR	51 - 173	51 - 173
86	43	43	THR	THR	THR	THR	51 - 173	51 - 173
87	44	44	VAL	VAL	GLY	GLY	52 - 172	52 - 172
88	44	44	VAL	VAL	GLY	GLY	52 - 172	52 - 172
89	45	45	VAL	VAL	GLY	GLY	52 - 172	52 - 172
90	45	45	VAL	VAL	GLY	GLY	52 - 172	52 - 172

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56
29	Local NCS retraints between domains: 57 58
30	Local NCS retraints between domains: 59 60
31	Local NCS retraints between domains: 61 62
32	Local NCS retraints between domains: 63 64
33	Local NCS retraints between domains: 65 66
34	Local NCS retraints between domains: 67 68
35	Local NCS retraints between domains: 69 70
36	Local NCS retraints between domains: 71 72
37	Local NCS retraints between domains: 73 74
38	Local NCS retraints between domains: 75 76
39	Local NCS retraints between domains: 77 78
40	Local NCS retraints between domains: 79 80
41	Local NCS retraints between domains: 81 82
42	Local NCS retraints between domains: 83 84
43	Local NCS retraints between domains: 85 86
44	Local NCS retraints between domains: 87 88
45	Local NCS retraints between domains: 89 90

#1: Protein

Killer cell lectin-like receptor subfamily F member 1 / Lectin-like receptor F1 / Activating coreceptor NKp80 / C-type lectin domain family 5 member C

Mass: 21030.859 Da / Num. of mol.: 10 / Mutation: C103S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: KLRF1, CLEC5C, ML / Cell line (production host): HEK293 / Production host:

Homo sapiens (human) / References: UniProt: Q9NZS2

#2: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#3: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

Has protein modification

Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 56.98 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.8M Succinic Acid 0.1M Tris

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P14 (MX2) / Wavelength: 0.9763 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9763 Å / Relative weight: 1

Reflection

Resolution: 2.9→158.95 Å / Num. obs: 49380 / % possible obs: 93.9 % / Redundancy: 9.2 % / CC_1/2: 0.962 / R_merge(I) obs: 0.641 / R_pim(I) all: 0.304 / R_rim(I) all: 0.714 / Net I/σ(I): 3.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
11.6-158.95	8.7	0.192	783	0.985	0.091	0.213
2.9-3	9.2		4590	0.026	5.579	12.872

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS	Jan 10, 2022 BUILT=20220820	data reduction
Aimless	0.7.13	data scaling
MOLREP	11.9.02	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→97.607 Å / Cor.coef. F_o:F_c: 0.931 / Cor.coef. F_o:F_c free: 0.911 / WR_factor R_free: 0.23 / WR_factor R_work: 0.194 / SU B: 58.574 / SU ML: 0.415 / Average fsc free: 0.9168 / Average fsc work: 0.9291 / Cross valid method: FREE R-VALUE / ESU R: 0.923 / ESU R Free: 0.364 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2572	2339	4.74 %
R_work	0.221	47010	-
all	0.223	-	-
obs	-	49349	93.893 %

Solvent computation

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

Displacement parameters

B_iso mean: 96.3 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.099 Å²	1.05 Å²	0 Å²
2-	-	2.099 Å²	-0 Å²
3-	-	-	-6.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→97.607 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10219	0	140	43	10402

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	10700
X-RAY DIFFRACTION	r_angle_refined_deg	2.413	1.647	14491
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.479	5	1220
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.44	5	20
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.197	10	1913
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.803	10	464
X-RAY DIFFRACTION	r_chiral_restr	0.188	0.2	1536
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	8238
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	4820
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	7318
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	221
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.291	0.2	106
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.28	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	8.786	5.142	4910
X-RAY DIFFRACTION	r_mcangle_it	13.585	9.245	6120
X-RAY DIFFRACTION	r_scbond_it	12.597	5.812	5790
X-RAY DIFFRACTION	r_scangle_it	18.245	10.3	8371
X-RAY DIFFRACTION	r_lrange_it	21.515	60.01	16348
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.082	0.05	4113
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.106	0.05	4073
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.094	0.05	4051
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.096	0.05	4084
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.089	0.05	4107
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.087	0.05	4079
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.091	0.05	4112
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.1	0.05	4061
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.086	0.05	4048
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.099	0.05	4066
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.092	0.05	4070
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.095	0.05	4061
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.087	0.05	4097
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.084	0.05	4069
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.083	0.05	4095
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.095	0.05	4064
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.082	0.05	4075
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.094	0.05	4102
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.097	0.05	4136
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.088	0.05	4097
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.102	0.05	4028
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.089	0.05	4155
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.098	0.05	4121
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.088	0.05	4117
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.083	0.05	4157
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.081	0.05	4144
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.097	0.05	4020
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.069	0.05	4143
X-RAY DIFFRACTION	r_ncsr_local_group_29	0.077	0.05	4098
X-RAY DIFFRACTION	r_ncsr_local_group_30	0.077	0.05	4109
X-RAY DIFFRACTION	r_ncsr_local_group_31	0.089	0.05	4181
X-RAY DIFFRACTION	r_ncsr_local_group_32	0.094	0.05	4069
X-RAY DIFFRACTION	r_ncsr_local_group_33	0.075	0.05	4167
X-RAY DIFFRACTION	r_ncsr_local_group_34	0.086	0.05	4131
X-RAY DIFFRACTION	r_ncsr_local_group_35	0.082	0.05	4122
X-RAY DIFFRACTION	r_ncsr_local_group_36	0.093	0.05	4077
X-RAY DIFFRACTION	r_ncsr_local_group_37	0.064	0.05	4152
X-RAY DIFFRACTION	r_ncsr_local_group_38	0.08	0.05	4113
X-RAY DIFFRACTION	r_ncsr_local_group_39	0.072	0.05	4093
X-RAY DIFFRACTION	r_ncsr_local_group_40	0.089	0.05	4081
X-RAY DIFFRACTION	r_ncsr_local_group_41	0.095	0.05	4052
X-RAY DIFFRACTION	r_ncsr_local_group_42	0.093	0.05	4037
X-RAY DIFFRACTION	r_ncsr_local_group_43	0.081	0.05	4172
X-RAY DIFFRACTION	r_ncsr_local_group_44	0.07	0.05	4145
X-RAY DIFFRACTION	r_ncsr_local_group_45	0.079	0.05	4082

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	C	X-RAY DIFFRACTION	Local ncs	0.08233	0.0501
1	2	C	X-RAY DIFFRACTION	Local ncs	0.08233	0.0501
2	3	C	X-RAY DIFFRACTION	Local ncs	0.10605	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.10605	0.0501
3	5	C	X-RAY DIFFRACTION	Local ncs	0.09388	0.0501
3	6	C	X-RAY DIFFRACTION	Local ncs	0.09388	0.0501
4	7	C	X-RAY DIFFRACTION	Local ncs	0.09638	0.0501
4	8	C	X-RAY DIFFRACTION	Local ncs	0.09638	0.0501
5	9	C	X-RAY DIFFRACTION	Local ncs	0.08931	0.0501
5	10	C	X-RAY DIFFRACTION	Local ncs	0.08931	0.0501
6	11	C	X-RAY DIFFRACTION	Local ncs	0.0873	0.0501
6	12	C	X-RAY DIFFRACTION	Local ncs	0.0873	0.0501
7	13	C	X-RAY DIFFRACTION	Local ncs	0.0907	0.0501
7	14	C	X-RAY DIFFRACTION	Local ncs	0.0907	0.0501
8	15	C	X-RAY DIFFRACTION	Local ncs	0.09957	0.0501
8	16	C	X-RAY DIFFRACTION	Local ncs	0.09957	0.0501
9	17	C	X-RAY DIFFRACTION	Local ncs	0.08564	0.0501
9	18	C	X-RAY DIFFRACTION	Local ncs	0.08564	0.0501
10	19	C	X-RAY DIFFRACTION	Local ncs	0.09882	0.0501
10	20	C	X-RAY DIFFRACTION	Local ncs	0.09882	0.0501
11	21	C	X-RAY DIFFRACTION	Local ncs	0.09206	0.0501
11	22	C	X-RAY DIFFRACTION	Local ncs	0.09206	0.0501
12	23	C	X-RAY DIFFRACTION	Local ncs	0.09459	0.0501
12	24	C	X-RAY DIFFRACTION	Local ncs	0.09459	0.0501
13	25	C	X-RAY DIFFRACTION	Local ncs	0.08749	0.0501
13	26	C	X-RAY DIFFRACTION	Local ncs	0.08749	0.0501
14	27	C	X-RAY DIFFRACTION	Local ncs	0.08411	0.0501
14	28	C	X-RAY DIFFRACTION	Local ncs	0.08411	0.0501
15	29	C	X-RAY DIFFRACTION	Local ncs	0.08327	0.0501
15	30	C	X-RAY DIFFRACTION	Local ncs	0.08327	0.0501
16	31	C	X-RAY DIFFRACTION	Local ncs	0.09531	0.0501
16	32	C	X-RAY DIFFRACTION	Local ncs	0.09531	0.0501
17	33	C	X-RAY DIFFRACTION	Local ncs	0.08198	0.0501
17	34	C	X-RAY DIFFRACTION	Local ncs	0.08198	0.0501
18	35	C	X-RAY DIFFRACTION	Local ncs	0.09382	0.0501
18	36	C	X-RAY DIFFRACTION	Local ncs	0.09382	0.0501
19	37	C	X-RAY DIFFRACTION	Local ncs	0.09703	0.0501
19	38	C	X-RAY DIFFRACTION	Local ncs	0.09703	0.0501
20	39	C	X-RAY DIFFRACTION	Local ncs	0.08754	0.0501
20	40	C	X-RAY DIFFRACTION	Local ncs	0.08754	0.0501
21	41	C	X-RAY DIFFRACTION	Local ncs	0.10173	0.0501
21	42	C	X-RAY DIFFRACTION	Local ncs	0.10173	0.0501
22	43	C	X-RAY DIFFRACTION	Local ncs	0.08854	0.0501
22	44	C	X-RAY DIFFRACTION	Local ncs	0.08854	0.0501
23	45	C	X-RAY DIFFRACTION	Local ncs	0.09751	0.0501
23	46	C	X-RAY DIFFRACTION	Local ncs	0.09751	0.0501
24	47	C	X-RAY DIFFRACTION	Local ncs	0.08776	0.0501
24	48	C	X-RAY DIFFRACTION	Local ncs	0.08776	0.0501
25	49	C	X-RAY DIFFRACTION	Local ncs	0.08297	0.0501
25	50	C	X-RAY DIFFRACTION	Local ncs	0.08297	0.0501
26	51	C	X-RAY DIFFRACTION	Local ncs	0.08113	0.0501
26	52	C	X-RAY DIFFRACTION	Local ncs	0.08113	0.0501
27	53	C	X-RAY DIFFRACTION	Local ncs	0.09737	0.0501
27	54	C	X-RAY DIFFRACTION	Local ncs	0.09737	0.0501
28	55	C	X-RAY DIFFRACTION	Local ncs	0.06909	0.0501
28	56	C	X-RAY DIFFRACTION	Local ncs	0.06909	0.0501
29	57	C	X-RAY DIFFRACTION	Local ncs	0.07686	0.0501
29	58	C	X-RAY DIFFRACTION	Local ncs	0.07686	0.0501
30	59	C	X-RAY DIFFRACTION	Local ncs	0.07707	0.0501
30	60	C	X-RAY DIFFRACTION	Local ncs	0.07707	0.0501
31	61	C	X-RAY DIFFRACTION	Local ncs	0.0893	0.0501
31	62	C	X-RAY DIFFRACTION	Local ncs	0.0893	0.0501
32	63	C	X-RAY DIFFRACTION	Local ncs	0.0945	0.0501
32	64	C	X-RAY DIFFRACTION	Local ncs	0.0945	0.0501
33	65	C	X-RAY DIFFRACTION	Local ncs	0.07535	0.0501
33	66	C	X-RAY DIFFRACTION	Local ncs	0.07535	0.0501
34	67	C	X-RAY DIFFRACTION	Local ncs	0.0856	0.0501
34	68	C	X-RAY DIFFRACTION	Local ncs	0.0856	0.0501
35	69	C	X-RAY DIFFRACTION	Local ncs	0.08191	0.0501
35	70	C	X-RAY DIFFRACTION	Local ncs	0.08191	0.0501
36	71	C	X-RAY DIFFRACTION	Local ncs	0.09281	0.0501
36	72	C	X-RAY DIFFRACTION	Local ncs	0.09281	0.0501
37	73	C	X-RAY DIFFRACTION	Local ncs	0.06351	0.0501
37	74	C	X-RAY DIFFRACTION	Local ncs	0.06351	0.0501
38	75	C	X-RAY DIFFRACTION	Local ncs	0.08019	0.0501
38	76	C	X-RAY DIFFRACTION	Local ncs	0.08019	0.0501
39	77	C	X-RAY DIFFRACTION	Local ncs	0.07183	0.0501
39	78	C	X-RAY DIFFRACTION	Local ncs	0.07183	0.0501
40	79	C	X-RAY DIFFRACTION	Local ncs	0.08855	0.0501
40	80	C	X-RAY DIFFRACTION	Local ncs	0.08855	0.0501
41	81	C	X-RAY DIFFRACTION	Local ncs	0.09476	0.0501
41	82	C	X-RAY DIFFRACTION	Local ncs	0.09476	0.0501
42	83	C	X-RAY DIFFRACTION	Local ncs	0.09303	0.0501
42	84	C	X-RAY DIFFRACTION	Local ncs	0.09303	0.0501
43	85	C	X-RAY DIFFRACTION	Local ncs	0.08076	0.0501
43	86	C	X-RAY DIFFRACTION	Local ncs	0.08076	0.0501
44	87	C	X-RAY DIFFRACTION	Local ncs	0.06954	0.0501
44	88	C	X-RAY DIFFRACTION	Local ncs	0.06954	0.0501
45	89	C	X-RAY DIFFRACTION	Local ncs	0.07914	0.0501
45	90	C	X-RAY DIFFRACTION	Local ncs	0.07914	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.9-2.975	0.451	152	0.456	3494	0.456	3857	0.696	0.709	94.5294	0.448
2.975-3.057	0.437	179	0.413	3397	0.414	3782	0.854	0.878	94.5531	0.406
3.057-3.145	0.432	146	0.393	3309	0.395	3659	0.815	0.873	94.4247	0.391
3.145-3.242	0.389	159	0.372	3219	0.373	3569	0.839	0.844	94.6484	0.372
3.242-3.348	0.377	149	0.338	3145	0.34	3468	0.9	0.917	94.9827	0.333
3.348-3.466	0.345	140	0.315	3032	0.316	3339	0.925	0.936	94.9985	0.307
3.466-3.596	0.318	155	0.26	2894	0.263	3224	0.932	0.96	94.572	0.245
3.596-3.743	0.249	133	0.225	2803	0.226	3110	0.966	0.971	94.4051	0.206
3.743-3.909	0.215	121	0.186	2683	0.187	2964	0.971	0.98	94.6019	0.164
3.909-4.099	0.238	114	0.172	2580	0.175	2865	0.968	0.983	94.0314	0.151
4.099-4.321	0.212	147	0.144	2391	0.147	2700	0.974	0.988	94	0.127
4.321-4.582	0.216	97	0.141	2308	0.144	2575	0.973	0.988	93.3981	0.124
4.582-4.898	0.174	137	0.124	2130	0.127	2419	0.982	0.991	93.7164	0.114
4.898-5.289	0.194	104	0.128	1984	0.131	2246	0.977	0.991	92.9653	0.12
5.289-5.792	0.204	108	0.153	1780	0.156	2074	0.978	0.987	91.0318	0.143
5.792-6.473	0.24	82	0.189	1637	0.192	1880	0.962	0.982	91.4362	0.176
6.473-7.469	0.222	79	0.173	1468	0.175	1670	0.968	0.984	92.6347	0.165
7.469-9.134	0.161	69	0.155	1236	0.155	1416	0.984	0.988	92.161	0.154
9.134-12.862	0.207	38	0.198	969	0.199	1106	0.978	0.985	91.0488	0.206
12.862-97.607	0.231	30	0.253	551	0.252	635	0.971	0.945	91.4961	0.323

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	2.2599	-0.4507	-0.5139	3.0877	-0.931	5.7321	0.0268	-0.1128	-0.087	-0.1793	-0.0595	0.1199	-0.0822	-0.1413	0.0328	0.0435	-0.0129	-0.0339	0.0935	-0.021	0.6768	-91.797	49.4634	16.2485
2	3.2503	-0.2753	-0.9759	3.3827	1.5043	3.5875	0.0582	-0.2687	0.0034	0.0827	0.0687	-0.1464	-0.057	0.2274	-0.1269	0.0415	-0.0726	0.0363	0.1581	0.016	0.8244	-64.7748	49.3941	24.4855
3	4.9718	-0.4771	1.0949	3.7608	-2.3442	6.1585	0.0178	-0.2849	0.0556	0.6543	0.1215	0.0249	0.0674	0.2282	-0.1393	0.5067	0.0411	0.1359	0.047	-0.0484	0.6887	-80.3209	28.8234	45.5344
4	3.4306	0.3808	2.3826	4.6647	0.5965	6.6143	0.0405	0.066	0.1626	0.1006	-0.0415	0.5469	0.2892	-0.9162	0.0009	0.1689	-0.1065	0.1356	0.2282	0.0747	0.7816	-104.1136	22.7674	31.142
5	5.4206	-1.0679	0.0789	1.1167	0.2354	2.0185	0.0381	0.3512	0.2362	-0.009	0.1201	0.0059	-0.0744	0.0444	-0.1582	0.108	-0.0466	0.0234	0.1205	0.0413	0.6924	-75.1883	40.0461	-9.8659
6	2.8583	-0.2304	0.127	3.3646	-0.6117	4.5494	-0.0047	-0.1058	0.0414	-0.0646	0.0355	-0.2797	0.1627	0.5008	-0.0308	0.0763	-0.0336	0.0373	0.1012	-0.005	0.7338	-51.1006	29.9759	0.718
7	2.8778	-0.8577	-0.2319	3.0928	-0.2726	4.9687	-0.0529	-0.1026	0.0874	0.0751	-0.0345	-0.008	0.0007	0.1271	0.0875	0.2768	0.0435	0.0968	0.0145	0.0247	0.6783	-76.6205	-1.969	34.8598
8	3.7528	-0.3904	-0.6159	3.231	-0.5857	6.2788	-0.273	0.3107	-0.3688	0.0001	0.0326	0.293	0.5523	-0.4604	0.2404	0.3864	-0.1866	0.055	0.1206	-0.0256	0.7049	-95.2185	-3.5165	13.4777
9	4.4459	-0.411	-1.7839	5.1511	0.067	5.4753	-0.1493	0.5641	-0.2519	-0.4308	0.0489	-0.1248	0.5185	-0.7932	0.1004	0.3007	-0.1791	-0.0023	0.1999	-0.1161	0.6087	-77.6932	7.0929	-12.51
10	2.0929	0.7971	0.3858	4.672	-2.5934	5.8303	-0.2144	0.0597	0.022	-0.1466	-0.0727	-0.4413	0.0786	0.2124	0.2871	0.3038	0.0079	0.0804	0.01	0.0382	0.7682	-58.1513	-1.2704	6.9507

Refinement TLS group

Selection: ALL

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