PDB-4rgn: Structure of Staphylococcal Enterotoxin B bound to two neutralizi...

ID or keywords:

Entry

Database: PDB / ID: 4rgn

Title

Structure of Staphylococcal Enterotoxin B bound to two neutralizing antibodies, 14G8 and 6D3

Components

14G8 heavy chain
14G8 light chain
6D3 heavy chain
6D3 light chain
Enterotoxin type B

Keywords

TOXIN/IMMUNE SYSTEM / Neutralizing antibody / Staphylococcal enterotoxin B / TOXIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

toxin activity / extracellular region / metal ion binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.698 Å

Authors

Franklin, M.C. / Dutta, K. / Varshney, A.K. / Goger, M.J. / Fries, B.C.

Citation

Journal: J.Biol.Chem. / Year: 2015
Title: Mechanisms mediating enhanced neutralization efficacy of staphylococcal enterotoxin B by combinations of monoclonal antibodies.
Authors: Dutta, K. / Varshney, A.K. / Franklin, M.C. / Goger, M. / Wang, X. / Fries, B.C.

History

Deposition	Sep 30, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 21, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 28, 2015	Group: Database references
Revision 1.2	Apr 1, 2015	Group: Database references
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	4rgn_validation.pdf.gz	496.5 KB	Display	wwPDB validaton report
Full document	4rgn_full_validation.pdf.gz	532.9 KB	Display
Data in XML	4rgn_validation.xml.gz	71.2 KB	Display
Data in CIF	4rgn_validation.cif.gz	98.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rg/4rgn ftp://data.pdbj.org/pub/pdb/validation_reports/rg/4rgn	HTTPS FTP

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Related structure data

Related structure data	4rgmC 4rgoSC 3gi8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6wio-1 4ya8-d 3vrl-d 2917 2852 2913 2915 4zxi-d 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) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

A: Enterotoxin type B

B: 14G8 heavy chain

C: 14G8 light chain

D: 6D3 heavy chain

E: 6D3 light chain

S: Enterotoxin type B

H: 14G8 heavy chain

L: 14G8 light chain

F: 6D3 heavy chain

G: 6D3 light chain

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

1

A: Enterotoxin type B

B: 14G8 heavy chain

C: 14G8 light chain

D: 6D3 heavy chain

E: 6D3 light chain

defined by author
124 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

S: Enterotoxin type B

H: 14G8 heavy chain

L: 14G8 light chain

F: 6D3 heavy chain

G: 6D3 light chain

defined by author
124 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	301.331, 109.818, 82.782
Angle α, β, γ (deg.)	90.00, 94.53, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1 / Refine code: 2

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	SER	SER	LYS	LYS	A	A	2 - 237	8 - 243
2	1	SER	SER	LYS	LYS	S	F	2 - 237	8 - 243
1	2	GLU	GLU	ALA	ALA	B	B	1 - 120	1 - 120
2	2	GLU	GLU	ALA	ALA	H	G	1 - 120	1 - 120
1	3	ALA	ALA	ARG	ARG	B	B	121 - 220	121 - 220
2	3	ALA	ALA	ARG	ARG	H	G	121 - 220	121 - 220
1	4	ASP	ASP	ALA	ALA	C	C	1 - 109	1 - 109
2	4	ASP	ASP	ALA	ALA	L	H	1 - 109	1 - 109
1	5	ASP	ASP	GLU	GLU	C	C	110 - 213	110 - 213
2	5	ASP	ASP	GLU	GLU	L	H	110 - 213	110 - 213
1	6	VAL	VAL	SER	SER	D	D	2 - 119	2 - 119
2	6	VAL	VAL	SER	SER	F	I	2 - 119	2 - 119
1	7	ALA	ALA	PRO	PRO	D	D	120 - 218	120 - 218
2	7	ALA	ALA	PRO	PRO	F	I	120 - 218	120 - 218
1	8	ASP	ASP	LYS	LYS	E	E	1 - 113	1 - 113
2	8	ASP	ASP	LYS	LYS	G	J	1 - 113	1 - 113
1	9	ARG	ARG	CYS	CYS	E	E	114 - 220	114 - 220
2	9	ARG	ARG	CYS	CYS	G	J	114 - 220	114 - 220

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9

Details

The pharmacologically relevant complex contains one 14G8 Fab, one 6D3 Fab, and one SEB monomer. There are two such complexes in the asymmetric unit of the crystal: one containing chains A,B,C,D,E; the other containing chains S,H,L,F,G.

#1: Protein	Enterotoxin type B / SEB / Staphylococcal enterotoxin B Mass: 28975.607 Da / Num. of mol.: 2 / Fragment: UNP residues 28-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: entB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01552
#2: Antibody	14G8 heavy chain Mass: 23783.713 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#3: Antibody	14G8 light chain Mass: 23589.906 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#4: Antibody	6D3 heavy chain Mass: 23647.461 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma
#5: Antibody	6D3 light chain Mass: 24359.883 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: hybridoma

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.75 Å³/Da / Density % sol: 55.24 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M phosphate/citrate, pH 4.2, 6.7% w/v PEG3000, 0.5 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.698→100 Å / Num. all: 74028 / Num. obs: 73214 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / R_merge(I) obs: 0.094 / Net I/σ(I): 19.9
Reflection shell	Resolution: 2.698→2.75 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.741 / Mean I/σ(I) obs: 1.8 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4RGO AND 3GI8

4rgo

3gi8

Resolution: 2.698→45.71 Å / Cor.coef. F_o:F_c: 0.904 / Cor.coef. F_o:F_c free: 0.872 / SU B: 31.27 / SU ML: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.003 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27756	3611	5 %	RANDOM
R_work	0.24005	-	-	-
obs	0.24195	72447	97.72 %	-
all	-	74137	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 52.094 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.31 Å²	0 Å²	0.32 Å²
2-	-	2.39 Å²	0 Å²
3-	-	-	-2.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.698→45.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16749	0	0	0	16749

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	17175
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	11426
X-RAY DIFFRACTION	r_angle_refined_deg	1.447	1.952	23364
X-RAY DIFFRACTION	r_angle_other_deg	0.999	3	27979
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.134	5	2128
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.088	24.53	724
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.246	15	2805
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.276	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	2597
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	18993
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3402
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	0.21	1.5	10688
X-RAY DIFFRACTION	r_mcbond_other	0.105	1.5	4306
X-RAY DIFFRACTION	r_mcangle_it	0.347	2	17381
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.558	3	6487
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.712	4.5	5983
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

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1269	TIGHT POSITIONAL	0.03	0.05
1	A	1770	MEDIUM POSITIONAL	0.02	0.5
1	A	1269	TIGHT THERMAL	0.06	0.5
1	A	1770	MEDIUM THERMAL	0.06	2
2	B	701	TIGHT POSITIONAL	0.03	0.05
2	B	868	MEDIUM POSITIONAL	0.03	0.5
2	B	701	TIGHT THERMAL	0.07	0.5
2	B	868	MEDIUM THERMAL	0.08	2
3	B	543	TIGHT POSITIONAL	0.03	0.05
3	B	604	MEDIUM POSITIONAL	0.03	0.5
3	B	543	TIGHT THERMAL	0.08	0.5
3	B	604	MEDIUM THERMAL	0.08	2
4	C	636	TIGHT POSITIONAL	0.03	0.05
4	C	781	MEDIUM POSITIONAL	0.03	0.5
4	C	636	TIGHT THERMAL	0.07	0.5
4	C	781	MEDIUM THERMAL	0.07	2
5	C	615	TIGHT POSITIONAL	0.03	0.05
5	C	752	MEDIUM POSITIONAL	0.03	0.5
5	C	615	TIGHT THERMAL	0.07	0.5
5	C	752	MEDIUM THERMAL	0.08	2
6	D	693	TIGHT POSITIONAL	0.04	0.05
6	D	814	MEDIUM POSITIONAL	0.02	0.5
6	D	693	TIGHT THERMAL	0.03	0.5
6	D	814	MEDIUM THERMAL	0.04	2
7	D	537	TIGHT POSITIONAL	0.01	0.05
7	D	586	MEDIUM POSITIONAL	0.01	0.5
7	D	537	TIGHT THERMAL	0.02	0.5
7	D	586	MEDIUM THERMAL	0.03	2
8	E	662	TIGHT POSITIONAL	0.02	0.05
8	E	797	MEDIUM POSITIONAL	0.02	0.5
8	E	662	TIGHT THERMAL	0.03	0.5
8	E	797	MEDIUM THERMAL	0.04	2
9	E	633	TIGHT POSITIONAL	0.02	0.05
9	E	775	MEDIUM POSITIONAL	0.02	0.5
9	E	633	TIGHT THERMAL	0.03	0.5
9	E	775	MEDIUM THERMAL	0.04	2

LS refinement shell

Resolution: 2.698→2.768 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.471	235	-
R_work	0.395	4969	-
obs	-	-	95.57 %

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	3.2109	0.7618	-0.1438	2.6122	0.125	5.6619	-0.0557	0.5957	-0.0699	-0.24	-0.0993	-0.1941	0.0401	-0.085	0.155	0.4157	0.0371	0.0238	0.3195	0.2043	0.3631	51.7382	-79.5968	-34.6502
2	3.666	-1.1311	-0.3948	3.3922	0.3458	5.8533	-0.1009	-0.6363	-0.0219	0.3933	-0.0408	-0.0789	-0.032	-0.1664	0.1417	0.4338	-0.0734	-0.0167	0.3377	0.2054	0.338	51.9464	-42.003	-39.9558
3	1.7114	1.4344	2.1088	3.1129	0.5164	6.3885	-0.0967	-0.0533	0.2101	0.1384	-0.0006	-0.1347	-0.3006	0.2645	0.0973	0.2859	-0.0277	0.0051	0.2279	0.1473	0.3135	61.8301	-85.1569	0.6835
4	1.9262	2.5396	0.0078	12.8504	0.2199	1.656	-0.0121	-0.0994	0.0034	-0.0416	-0.0311	-0.3232	-0.0686	0.2671	0.0432	0.329	0.0024	-0.001	0.3003	0.1421	0.2239	64.6594	-111.5656	19.3029
5	2.2895	-1.3977	-2.0268	2.9387	0.119	5.0754	-0.1139	0.0918	-0.2412	-0.0423	-0.0169	-0.1759	0.3531	0.2697	0.1307	0.3055	-0.0015	0.012	0.2315	0.1415	0.3153	67.7653	-36.2131	-73.5826
6	1.9579	-3.0094	-0.0021	11.8693	0.2377	1.7623	-0.0309	0.0782	0.0095	0.0439	0.0167	-0.2848	0.0685	0.1826	0.0142	0.3173	-0.0392	0.0173	0.2906	0.1343	0.2338	73.3096	-9.7117	-91.5305
7	3.0981	2.5181	0.2381	4.901	-2.5936	3.0262	-0.0689	0.0148	0.1866	-0.1551	0.0571	0.3407	0.0373	-0.1808	0.0118	0.289	0.0458	0.0683	0.3261	0.1289	0.2691	41.8819	-93.4855	-1.8755
8	5.166	-0.2625	7.4074	1.6093	-1.8448	16.1107	-0.1287	-0.6114	0.0513	0.3776	0.1083	0.1515	-0.4709	-0.6606	0.0204	0.3969	0.0105	0.0737	0.2936	0.1161	0.2321	50.6002	-112.8544	28.1561
9	3.7501	-2.449	-0.0038	5.8758	-3.4945	2.6758	-0.0286	-0.0279	-0.2436	0.0483	0.1457	0.4313	-0.0355	-0.2145	-0.1172	0.3002	-0.0604	-0.0449	0.3183	0.1159	0.2508	47.6591	-27.7675	-74.1226
10	6.8496	0.3465	-7.9144	1.5147	-1.0715	11.7996	-0.1464	0.6591	-0.1025	-0.346	0.0733	0.0491	0.338	-0.5124	0.0731	0.3946	-0.0085	-0.034	0.2989	0.1255	0.2215	60.8831	-8.4512	-102.4626
11	13.0073	1.3604	-3.7042	6.4619	-3.0103	4.5811	-0.3744	0.2988	-1.6484	-0.8298	0.1224	0.6738	0.8093	-0.1212	0.2519	0.4946	-0.1439	-0.1514	0.692	0.0543	0.8764	20.0466	-98.5666	-26.4903
12	19.4346	-1.6891	1.2929	6.2853	-3.2619	4.8565	0.2183	2.3625	-0.4501	-1.2198	-0.7703	-0.9168	0.6214	0.3641	0.552	0.6585	0.114	0.2119	1.3083	0.2099	0.8157	-11.0034	-100.6634	-20.0044
13	8.8155	-0.277	4.5241	6.3539	-3.593	6.2458	-0.4488	-0.2151	1.5627	0.7604	0.0306	0.9091	-0.988	-0.2502	0.4182	0.5054	0.1835	0.0784	0.762	0.0878	0.9873	22.1765	-22.6888	-53.2875
14	21.2357	2.8659	1.9573	7.9933	-3.7108	3.1056	0.1988	-2.9038	0.4646	1.3777	-0.8902	-0.6644	-0.5879	0.0403	0.6913	0.7785	-0.1486	-0.191	1.314	0.0892	0.7661	-7.4728	-20.6664	-64.5306
15	13.1392	0.0886	-2.2181	6.4351	-1.3671	2.7013	0.538	0.3926	1.9762	0.0931	0.2989	1.3814	-0.6177	-0.435	-0.8369	0.4959	-0.0902	0.035	0.8035	0.3194	1.0974	15.3916	-76.7011	-27.3929
16	18.1384	5.1523	-7.4663	8.7682	-6.3754	6.8753	1.099	-0.5487	2.2617	0.8645	-0.9615	-0.7765	-0.7986	0.8541	-0.1374	0.4362	-0.1046	0.0228	0.8033	0.006	1.0306	-16.3662	-89.7956	-8.3484
17	10.3424	-0.2959	2.7668	7.0184	-2.6665	3.5424	0.5775	-0.3963	-1.8371	-0.3117	0.4137	1.4262	0.8279	-0.6839	-0.9912	0.5617	0.053	-0.1087	0.8793	0.3103	1.1157	17.4269	-44.5587	-53.1111
18	15.5958	-4.4258	9.2536	8.2085	-7.1532	9.8956	1.2205	0.5085	-2.009	-0.6571	-0.9386	-0.8276	0.9541	1.0183	-0.2819	0.4815	0.0958	-0.0895	0.841	-0.0051	1.0378	-10.9841	-31.5006	-76.8787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 237
2	X-RAY DIFFRACTION	2	S	2 - 238
3	X-RAY DIFFRACTION	3	B	1 - 120
4	X-RAY DIFFRACTION	4	B	121 - 220
5	X-RAY DIFFRACTION	5	H	1 - 120
6	X-RAY DIFFRACTION	6	H	121 - 220
7	X-RAY DIFFRACTION	7	C	1 - 109
8	X-RAY DIFFRACTION	8	C	110 - 213
9	X-RAY DIFFRACTION	9	L	1 - 109
10	X-RAY DIFFRACTION	10	L	110 - 213
11	X-RAY DIFFRACTION	11	D	2 - 119
12	X-RAY DIFFRACTION	12	D	120 - 218
13	X-RAY DIFFRACTION	13	F	2 - 119
14	X-RAY DIFFRACTION	14	F	120 - 218
15	X-RAY DIFFRACTION	15	E	1 - 113
16	X-RAY DIFFRACTION	16	E	114 - 220
17	X-RAY DIFFRACTION	17	G	1 - 113
18	X-RAY DIFFRACTION	18	G	114 - 220

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