PDB-2vxs: Structure of IL-17A in complex with a potent, fully human neutral...

ID or keywords:

Entry

Database: PDB / ID: 2vxs

Title

Structure of IL-17A in complex with a potent, fully human neutralising antibody

Components

(FAB FRAGMENT) x 2
INTERLEUKIN-17A

Keywords

CYTOKINE / EPITOPE / COMPLEX / ANTIBODY / SECRETED / GLYCOPROTEIN / INTERLEUKIN-17

Function / homology

Function and homology information

positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.63 Å

Authors

Gerhardt, S. / Hargreaves, D. / Pauptit, R.A. / Davies, R.A. / Russell, C. / Welsh, F. / Tuske, S.J. / Coales, S.J. / Hamuro, Y. / Needham, M.R.C. ...

Citation

Journal: J.Mol.Biol. / Year: 2009
Title: Structure of Il-17A in Complex with a Potent, Fully Human Neutralising Antibody.
Authors: Gerhardt, S. / Abbott, W.M. / Hargreaves, D. / Pauptit, R.A. / Davies, R.A. / Needham, M.R. / Langham, C. / Barker, W. / Aziz, A. / Snow, M.J. / Dawson, S. / Welsh, F. / Wilkinson, T. / ...

History

Deposition	Jul 9, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 14, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2vxs.cif.gz	393.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2vxs.ent.gz	320.1 KB	Display	PDB format
PDBx/mmJSON format	2vxs.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/vx/2vxs ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vxs	HTTPS FTP

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Related structure data

Related structure data	1aqkS S: Starting model for refinement
Similar structure data	4edx-d 7czf-1 4jkx-1 5w3w-d 7cze-1 6o9i-d 3t1w-1 6a0p-1 2fss-3 1sz6-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #68 - Aug 2005 Neurotrophins similarity (1)

Deposited unit

A: INTERLEUKIN-17A

B: INTERLEUKIN-17A

C: INTERLEUKIN-17A

D: INTERLEUKIN-17A

H: FAB FRAGMENT

I: FAB FRAGMENT

J: FAB FRAGMENT

K: FAB FRAGMENT

L: FAB FRAGMENT

M: FAB FRAGMENT

N: FAB FRAGMENT

O: FAB FRAGMENT

hetero molecules

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

1

C: INTERLEUKIN-17A

D: INTERLEUKIN-17A

J: FAB FRAGMENT

K: FAB FRAGMENT

N: FAB FRAGMENT

O: FAB FRAGMENT

hetero molecules

defined by author&software
126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: INTERLEUKIN-17A

B: INTERLEUKIN-17A

H: FAB FRAGMENT

I: FAB FRAGMENT

L: FAB FRAGMENT

M: FAB FRAGMENT

hetero molecules

defined by author&software
126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.473, 66.708, 203.790
Angle α, β, γ (deg.)	90.00, 91.65, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	H
2	1	I
3	1	J
4	1	K
1	2	L
2	2	M
3	2	N
4	2	O
1	3	A
2	3	B
3	3	C
4	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	H	1 - 213
2	1	1	5	I	1 - 213
3	1	1	5	J	1 - 213
4	1	1	5	K	1 - 213
1	1	2	5	L	1 - 210
3	1	2	5	N	1 - 210
2	1	2	5	M	1 - 210
4	1	2	5	O	1 - 210
1	1	3	5	A	1 - 128
2	1	3	5	B	1 - 128
3	1	3	5	C	1 - 128
4	1	3	5	D	1 - 128

NCS ensembles :

ID
1
2
3

#1: Protein	INTERLEUKIN-17A / IL-17A / IL-17 / CYTOTOXIC T-LYMPHOCYTE- ASSOCIATED ANTIGEN 8 / CTLA-8 / INTERLEUKINE-17A Mass: 15689.864 Da / Num. of mol.: 4 / Fragment: RESIDUES 20-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q16552
#2: Antibody	FAB FRAGMENT Mass: 23671.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#3: Antibody	FAB FRAGMENT Mass: 23196.564 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Sequence details	SWISSPROT ACCESSION NUMBER Q16552. THE NUMBERING OF THE FAB-FRAGMENT (CHAINS H,I,J,K AND L,M,N,O) ...SWISSPROT ACCESSION NUMBER Q16552. THE NUMBERING OF THE FAB-FRAGMENT (CHAINS H,I,J,K AND L,M,N,O) ARE ACCORDING TO THE NOMENCLATURE OF KABAT ET AL

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	Details: 90.9 MM PCTP BUFFER PH 4.0, 9.1 MM PCTP BUFFER PH 9.5, 100 MM AMMONIUM SULPHATE, 14% W/V PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9787
Detector	Type: ADSC CCD / Detector: CCD / Date: Apr 30, 2007 / Details: TOROIDAL MIRROR
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9787 Å / Relative weight: 1
Reflection	Resolution: 2.63→102.1 Å / Num. obs: 79235 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7 % / R_merge(I) obs: 0.13 / Net I/σ(I): 11.7
Reflection shell	Resolution: 2.63→2.77 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0036	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQK

1aqk

Resolution: 2.63→204.12 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.868 / SU B: 24.577 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.635 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.264	3976	5 %	RANDOM
R_work	0.213	-	-	-
obs	0.215	75243	99.9 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 19.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.49 Å²	0 Å²	-1.72 Å²
2-	-	-1.56 Å²	0 Å²
3-	-	-	-0.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.63→204.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15395	0	60	214	15669

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	15829
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	1.956	21603
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.672	5	2022
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.263	24.017	595
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.628	15	2438
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.308	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2449
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	11874
X-RAY DIFFRACTION	r_gen_planes_other
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	0.355	1.5	10170
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.644	2	16481
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.888	3	5659
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.394	4.5	5122
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	H	844	medium positional	0.65	0.5
1	2	I	844	medium positional	0.52	0.5
1	3	J	844	medium positional	0.47	0.5
1	4	K	844	medium positional	0.55	0.5
2	1	L	848	medium positional	0.39	0.5
2	2	M	848	medium positional	0.31	0.5
2	3	N	848	medium positional	0.31	0.5
2	4	O	848	medium positional	0.34	0.5
3	1	A	300	medium positional	0.25	0.5
3	2	B	300	medium positional	0.25	0.5
3	3	C	300	medium positional	0.27	0.5
3	4	D	300	medium positional	0.28	0.5
1	1	H	717	loose positional	0.82	5
1	2	I	717	loose positional	0.72	5
1	3	J	717	loose positional	0.68	5
1	4	K	717	loose positional	0.69	5
2	1	L	753	loose positional	0.64	5
2	2	M	753	loose positional	0.6	5
2	3	N	753	loose positional	0.61	5
2	4	O	753	loose positional	0.66	5
3	1	A	297	loose positional	0.62	5
3	2	B	297	loose positional	0.75	5
3	3	C	297	loose positional	0.77	5
3	4	D	297	loose positional	0.69	5
1	1	H	844	medium thermal	0.43	2
1	2	I	844	medium thermal	0.44	2
1	3	J	844	medium thermal	0.36	2
1	4	K	844	medium thermal	0.45	2
2	1	L	848	medium thermal	0.35	2
2	2	M	848	medium thermal	0.27	2
2	3	N	848	medium thermal	0.36	2
2	4	O	848	medium thermal	0.36	2
3	1	A	300	medium thermal	0.42	2
3	2	B	300	medium thermal	0.35	2
3	3	C	300	medium thermal	0.41	2
3	4	D	300	medium thermal	0.3	2
1	1	H	717	loose thermal	0.87	10
1	2	I	717	loose thermal	0.82	10
1	3	J	717	loose thermal	0.54	10
1	4	K	717	loose thermal	0.74	10
2	1	L	753	loose thermal	0.54	10
2	2	M	753	loose thermal	0.43	10
2	3	N	753	loose thermal	0.53	10
2	4	O	753	loose thermal	0.58	10
3	1	A	297	loose thermal	0.69	10
3	2	B	297	loose thermal	0.51	10
3	3	C	297	loose thermal	0.75	10
3	4	D	297	loose thermal	0.48	10

LS refinement shell

Resolution: 2.63→2.7 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.332	297	-
R_work	0.253	5433	-
obs	-	-	98.25 %

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	4.1069	-0.3823	-0.092	1.5791	0.0826	1.0894	0.075	0.1042	0.0354	-0.1769	-0.0847	-0.09	0.014	0.0098	0.0096	0.1104	0.0021	0.0302	0.1548	0.032	0.1887	113.2523	-0.8011	-29.981
2	3.0577	2.0398	-0.9525	3.8354	-0.7893	2.1827	0.0637	0.0863	-0.3725	-0.2397	0.0148	-0.0604	0.4257	-0.2668	-0.0785	0.2107	-0.044	-0.0626	0.2151	0.0769	0.335	122.299	-30.6071	-25.9188
3	1.3308	-0.5522	0.7437	3.9703	-1.3181	2.1327	-0.0119	-0.2247	0.0583	0.2999	-0.111	-0.0629	-0.0146	-0.2394	0.123	0.095	-0.0966	0.019	0.2514	-0.0208	0.1323	105.9176	-1.3621	-9.1952
4	3.0383	-0.7142	-0.7841	2.4124	0.2542	2.0651	0.0952	-0.1712	-0.3151	0.0135	-0.0421	-0.0193	0.2273	0.0654	-0.0531	0.1114	-0.0893	-0.0753	0.1458	0.1463	0.2353	130.3353	-31.4628	-11.4917
5	3.3518	-1.0525	-0.093	1.8288	0.075	1.2083	-0.0673	0.086	0.1072	-0.1248	0.0361	0.0172	-0.0276	0.0278	0.0312	0.1727	-0.0157	-0.0471	0.0978	-0.009	0.1503	66.169	31.9504	-31.1849
6	1.4454	1.8466	0.7444	3.7832	-0.2836	1.6006	-0.0457	-0.033	0.0262	-0.078	0.0873	0.0369	0.0133	-0.0126	-0.0416	0.062	0.0324	0.02	0.1025	-0.035	0.1635	58.4317	64.4989	-30.7628
7	0.8429	0.3768	0.1465	3.5794	0.8271	1.1578	-0.1682	-0.1779	0.1193	0.054	0.1013	-0.1314	-0.0332	-0.0301	0.0669	0.1128	0.0633	-0.0619	0.1581	-0.052	0.1622	76.2907	36.037	-11.7471
8	3.4768	-0.9247	2.1171	1.9692	-0.7698	3.7868	0.0622	-0.0704	0.1616	0.151	0.0409	0.0016	-0.0436	-0.1156	-0.1031	0.0365	0.0149	0.0354	0.0663	-0.024	0.0897	52.0811	66.5542	-15.9861
9	2.6508	0.5877	-0.973	2.1846	-0.6313	2.8323	0.0308	-0.0385	0.0813	-0.0387	-0.1979	-0.4202	0.0794	0.3318	0.1671	0.2787	0.0292	0.0194	0.3832	0.05	0.3352	84.786	-8.1587	-92.7582
10	4.8919	-2.673	-0.6978	5.0427	0.6905	1.5416	-0.1416	-0.4425	0.4126	0.3285	0.0873	-0.3475	-0.3977	-0.1362	0.0543	0.5187	0.081	-0.0174	0.5258	0.008	0.4465	88.2008	20.933	-102.3358
11	2.2851	-0.9722	1.116	3.8443	-1.6281	2.6723	0.097	0.0061	-0.1212	-0.2992	-0.1275	0.2826	0.1659	-0.2301	0.0305	0.2724	0.0512	0.0065	0.3611	-0.0961	0.1608	64.4522	-7.3669	-101.4024
12	2.8259	0.1713	-0.4069	3.3345	-0.2114	2.5929	-0.0585	0.5506	0.3409	-0.1905	-0.0136	-0.1818	-0.4405	0.074	0.0721	0.4894	0.0827	-0.0117	0.5171	0.0651	0.3331	82.6159	22.5404	-118.055
13	2.066	0.7427	-0.7255	1.8886	-0.967	2.0681	-0.0165	0.0181	-0.0414	0.018	0.0254	-0.0742	0.0521	0.1046	-0.0089	0.3065	0.0314	-0.029	0.1458	-0.0249	0.1265	54.3974	-41.4758	-57.4069
14	0.7182	-1.1781	-0.2491	5.5751	2.0737	2.6568	-0.0255	0.1146	0.0573	-0.2001	0.0724	0.1328	-0.0696	-0.0539	-0.0469	0.1675	-0.0232	0.0193	0.0882	0.0103	0.102	48.8883	-73.3439	-51.7623
15	1.2629	0.5619	0.7587	3.1067	0.5166	1.8336	0.0404	0.2118	-0.0494	-0.2316	0.0492	-0.0225	0.2856	-0.0672	-0.0896	0.33	-0.005	-0.0193	0.1822	-0.014	0.1016	46.8362	-45.4845	-77.9642
16	1.7311	0.0265	-0.4576	2.7033	-0.9508	5.6314	-0.1217	0.1266	-0.1039	-0.3525	0.0732	0.3733	-0.022	-0.2016	0.0485	0.1601	-0.0406	-0.0921	0.0955	0.0103	0.2113	33.6491	-75.9459	-57.2492
17	2.5097	-0.9289	-1.2358	3.8839	2.0292	4.2612	-0.1301	0.4172	-0.2409	-0.4336	0.0261	0.1023	0.1728	-0.1999	0.104	0.1315	-0.0231	-0.0553	0.215	-0.0563	0.2387	83.7452	10.3533	-37.5294
18	2.4132	-0.7008	0.4319	2.7945	-0.4584	2.9572	-0.0073	0.3976	0.2647	-0.5306	-0.0656	-0.1563	-0.1515	-0.0005	0.0729	0.1532	-0.0297	0.0569	0.2137	-0.0183	0.201	94.9125	17.9148	-37.6337
19	4.1687	1.9481	0.2493	3.1242	0.6239	1.2288	0.0916	-0.4063	0.0477	0.2772	-0.0018	-0.3097	-0.2454	0.3017	-0.0897	0.3827	-0.0172	0.012	0.3383	-0.0165	0.139	70.271	-20.044	-66.6011
20	2.0587	1.0419	0.2497	3.1652	-0.4019	3.5909	-0.0303	-0.2253	-0.1763	0.1997	-0.0769	-0.5039	0.1692	0.4276	0.1072	0.24	0.0416	0.0642	0.3482	-0.038	0.2913	77.89	-27.5661	-74.9587

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	H	1 - 118
2	X-RAY DIFFRACTION	2	H	119 - 216
3	X-RAY DIFFRACTION	3	L	2 - 112
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