PDB-4wfh: Human TRAAK K+ channel in a Tl+ bound nonconductive conformation

ID or keywords:

Entry

Database: PDB / ID: 4wfh

Title

Human TRAAK K+ channel in a Tl+ bound nonconductive conformation

Components

(ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT ...) x 2
Potassium channel subfamily K member 4

Keywords

METAL TRANSPORT / Mechanosensitive ion channel / two-pore domain potassium ion channel / membrane protein

Function / homology

Function and homology information

mechanosensitive potassium channel activity / TWIK related potassium channel (TREK) / temperature-gated cation channel activity / sensory perception of temperature stimulus / detection of mechanical stimulus involved in sensory perception of touch / Phase 4 - resting membrane potential / potassium channel complex / cellular response to alkaline pH / stabilization of membrane potential / potassium ion leak channel activity ...
Similarity search - Function

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.01 Å

Authors

Brohawn, S.G. / MacKinnon, R.

Citation

Journal: Nature / Year: 2014
Title: Physical mechanism for gating and mechanosensitivity of the human TRAAK K+ channel.
Authors: Brohawn, S.G. / Campbell, E.B. / MacKinnon, R.

History

Deposition	Sep 15, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 17, 2014	Group: Database references
Revision 1.2	Feb 4, 2015	Group: Derived calculations
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn / struct_keywords / struct_ncs_dom_lim Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_keywords.text / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

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Validation report

Summary document	4wfh_validation.pdf.gz	491.3 KB	Display	wwPDB validaton report
Full document	4wfh_full_validation.pdf.gz	514 KB	Display
Data in XML	4wfh_validation.xml.gz	49.5 KB	Display
Data in CIF	4wfh_validation.cif.gz	68.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wf/4wfh ftp://data.pdbj.org/pub/pdb/validation_reports/wf/4wfh	HTTPS FTP

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Related structure data

Related structure data	4wfeC 4wffC 4wfgC C: citing same article (ref.)
Similar structure data	4wfg-d 4i9w-d 4wfe-d 2cge-d 4wff-d 2y4u-2 3t0e-d 4e3c-2 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	#223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (7) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #38 - Feb 2003 Potassium Channels similarity (2)

Deposited unit

A: Potassium channel subfamily K member 4

B: Potassium channel subfamily K member 4

D: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN

E: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN

F: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN

G: ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN

hetero molecules

160 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	80.972, 138.755, 96.759
Angle α, β, γ (deg.)	90.00, 94.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	D
2	2	F
1	3	E
2	3	G

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	ARG	ARG	ALA	ALA	A	A	28 - 273	28 - 273
2	1	ARG	ARG	ALA	ALA	B	B	28 - 273	28 - 273
1	2	GLN	GLN	ASN	ASN	D	C	1 - 211	1 - 211
2	2	GLN	GLN	ASN	ASN	F	E	1 - 211	1 - 211
1	3	GLU	GLU	PRO	PRO	E	D	1 - 215	1 - 215
2	3	GLU	GLU	PRO	PRO	G	F	1 - 215	1 - 215

NCS ensembles :

ID
1
2
3

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Protein , 1 types, 2 molecules AB

#1: Protein	Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium ...TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium channel KT4.1 / Two pore K(+) channel KT4.1 Mass: 32569.650 Da / Num. of mol.: 2 / Mutation: N104Q, N108Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KCNK4, TRAAK / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9NYG8

#1: Protein

Potassium channel subfamily K member 4 / TWIK-related arachidonic acid-stimulated potassium channel protein / TRAAK / Two pore potassium ...

Mass: 32569.650 Da / Num. of mol.: 2 / Mutation: N104Q, N108Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: KCNK4, TRAAK / Production host:

Komagataella pastoris (fungus) / References: UniProt: Q9NYG8

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Antibody , 2 types, 4 molecules DFEG

#2: Antibody	ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN Mass: 23038.404 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody	ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN Mass: 23474.381 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 195 molecules

#4: Chemical	ChemComp-TL / THALLIUM (I) ION Mass: 204.383 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Tl
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-D10 / DECANE Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.43 Å³/Da / Density % sol: 64.09 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 50 MM TRIS PH 8.8, 200 MM CA(NO3)2, 27-30% (VOL/VOL) PEG400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9781 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9781 Å / Relative weight: 1
Reflection	Resolution: 3→48.2 Å / Num. obs: 39746 / % possible obs: 100 % / Redundancy: 10.5 % / Net I/σ(I): 11.3
Reflection shell	Resolution: 3→3.05 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 0.6 / % possible all: 100

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Processing

Software

Name: REFMAC / Version: 5.8.0073 / Classification: refinement

Refinement

Resolution: 3.01→48.2 Å / Cor.coef. F_o:F_c: 0.906 / Cor.coef. F_o:F_c free: 0.917 / SU B: 47.469 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2385	2098	5 %	RANDOM
R_work	0.20321	-	-	-
obs	0.20502	39746	99 %	-

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 mean: 112.451 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.54 Å²	0 Å²	3.38 Å²
2-	-	-3.27 Å²	0 Å²
3-	-	-	3.22 Å²

Refinement step

Cycle: 1 / Resolution: 3.01→48.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10302	0	20	184	10506

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.02	10580
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9860
X-RAY DIFFRACTION	r_angle_refined_deg	0.908	1.955	14415
X-RAY DIFFRACTION	r_angle_other_deg	0.608	3	22756
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.707	5	1328
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.475	23.731	402
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.735	15	1676
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.32	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	1642
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	11839
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2392
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	4.923	5.264	5345
X-RAY DIFFRACTION	r_mcbond_other	4.922	5.264	5344
X-RAY DIFFRACTION	r_mcangle_it	7.563	7.892	6662
X-RAY DIFFRACTION	r_mcangle_other	7.562	7.893	6663
X-RAY DIFFRACTION	r_scbond_it	5.637	5.674	5235
X-RAY DIFFRACTION	r_scbond_other	5.637	5.676	5236
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	8.686	8.342	7754
X-RAY DIFFRACTION	r_long_range_B_refined	13.568	50.719	43753
X-RAY DIFFRACTION	r_long_range_B_other	13.569	50.721	43754
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 / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	12265	0.14
1	2	B	12265	0.14
2	1	D	11182	0.1
2	2	F	11182	0.1
3	1	E	11473	0.1
3	2	G	11473	0.1

LS refinement shell

Resolution: 3.01→3.088 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	130	-
R_work	0.371	2602	-
obs	-	-	87.73 %

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	4.1055	-1.0816	-3.6461	0.371	0.6158	5.157	0.4635	0.4558	0.0716	-0.1477	-0.2239	0.121	-0.5048	0.3811	-0.2397	0.5772	-0.0375	0.1753	0.4051	0.062	0.7936	44.264	-5.835	10.095
2	0.3435	-0.1557	0.0364	0.1686	-0.911	11.6479	0.0331	0.6231	-0.2077	-0.2798	-0.2916	0.1462	1.1768	0.264	0.2585	1.5127	0.133	0.0717	1.1618	-0.2177	1.0157	49.951	-20.415	-20.775
3	7.9924	-0.5254	-1.414	7.0066	-0.051	4.1332	-0.4132	0.9908	-0.7603	-0.8016	0.1924	0.0653	1.025	-0.4818	0.2209	0.852	0.132	-0.0702	0.8238	-0.1146	0.738	45.668	-16.753	-6.594
4	4.0644	-0.4037	-3.8786	0.8048	-0.8899	6.3013	0.5134	0.4351	0.1694	-0.2245	-0.2921	0.0446	-0.548	0.3513	-0.2213	0.5471	-0.0568	0.1233	0.4533	-0.0228	0.6956	47.875	-10.155	7.327
5	3.972	1.2147	1.7362	10.8047	-3.7571	2.5272	-0.5903	0.1539	0.0662	-0.1255	0.7429	0.2507	-0.2523	-0.198	-0.1526	1.3646	0.055	0.0715	1.6981	-0.1789	1.4927	92.149	-4.559	-4.801
6	7.1537	1.2524	2.3501	2.962	-1.2326	8.8084	0.6886	0.2718	0.991	0.1049	-0.2106	-1.014	-1.3328	1.0909	-0.4779	0.8679	-0.0847	0.2305	0.8688	0.066	1.0981	64.37	-2.727	5.524
7	3.8983	-1.7157	1.012	5.8509	0.1426	7.3612	-0.1517	0.3275	0.432	-0.9641	-0.3524	0.3129	-0.9861	-0.3664	0.5041	0.4027	0.0779	-0.0722	0.0621	-0.0005	0.5201	14.178	16.476	27.064
8	6.3919	4.2882	6.7384	6.2846	5.9698	9.0235	-0.1802	0.6851	0.3258	-1.1856	-0.1739	0.1891	-0.6436	0.905	0.354	0.5847	0.1849	-0.0904	0.3461	0.0461	0.8796	12.927	46.387	46.137
9	4.3865	2.3862	3.1653	7.1849	5.2082	7.8204	0.055	0.5813	0.3764	-0.6427	-0.2286	0.1252	-0.6285	0.4533	0.1736	0.615	0.0911	-0.0232	0.1686	0.043	0.8688	13.411	47.46	46.114
10	3.4398	-0.7592	0.2237	6.8483	4.5388	8.1152	-0.3318	-0.1525	0.2206	0.3889	0.0026	0.2396	-0.101	0.4893	0.3292	0.0773	-0.0095	0.063	0.0671	0.0526	0.5043	24.936	6.527	45.274
11	1.1341	-1.6062	-1.5596	7.5372	3.2977	2.3927	0.1424	-0.3124	0.0139	-0.2428	-0.304	0.4007	-0.2423	0.2663	0.1616	0.1923	0.0283	-0.0204	0.2149	-0.0455	0.5903	19.325	22.137	49.269
12	10.1407	-5.317	-0.172	6.5734	1.1285	2.7047	0.1589	-0.4214	0.0771	0.1387	-0.1186	0.6478	-0.2445	-0.1585	-0.0403	0.2398	-0.04	-0.0174	0.0564	-0.0855	0.8197	7.32	37.127	58.26
13	5.8166	0.086	0.1175	7.6275	-2.771	3.2842	0.0265	-0.2783	-0.4823	0.2843	-0.0619	-0.4358	0.0291	0.0955	0.0354	0.0386	0.0033	0.0676	0.0212	0.0072	0.6264	29.728	-34.984	42.241
14	5.4113	2.6611	2.6212	2.6908	1.1702	3.478	0.0953	0.5331	-0.2636	-0.3208	0.0493	-0.1557	0.3781	0.0416	-0.1446	0.4938	0.0927	-0.0423	0.2671	0.1148	0.8299	8.795	-63.207	43.936
15	0.2479	0.9409	0.3689	6.0902	-0.5005	3.3172	0.3524	-0.1418	-0.0518	0.3699	-0.1743	0.4263	1.6169	-0.011	-0.178	1.0146	-0.1322	-0.1485	0.4953	0.0774	1.5406	11.876	-72.056	46.651
16	6.6735	2.6313	-0.793	7.3077	-0.9607	3.4119	-0.0312	0.3637	-0.0561	-0.1529	0.2293	0.6071	-0.0178	-0.193	-0.198	0.075	0.0481	0.0434	0.0624	0.0487	0.4305	11.773	-25.24	31.134
17	4.3634	3.141	-1.3572	5.7205	-1.1913	0.9337	-0.0506	-0.0185	-0.7631	-0.0183	0.0197	0.0602	0.1605	-0.1865	0.031	0.0497	-0.0545	0.0246	0.0741	0.0718	0.967	5.005	-45.085	42.035
18	3.1725	-0.6341	1.9149	5.3415	-4.7262	8.8657	-0.2105	-0.3566	-0.0263	0.1042	0.2163	0.2493	0.2779	-0.37	-0.0058	0.2491	-0.0481	0.0035	0.3777	0.0275	0.746	-3.539	-55.617	50.52

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	28 - 148
2	X-RAY DIFFRACTION	2	A	149 - 219
3	X-RAY DIFFRACTION	3	A	220 - 286
4	X-RAY DIFFRACTION	4	B	28 - 175
5	X-RAY DIFFRACTION	5	B	176 - 197
6	X-RAY DIFFRACTION	6	B	198 - 274
7	X-RAY DIFFRACTION	7	D	1 - 105
8	X-RAY DIFFRACTION	8	D	106 - 157
9	X-RAY DIFFRACTION	9	D	158 - 211
10	X-RAY DIFFRACTION	10	E	1 - 80
11	X-RAY DIFFRACTION	11	E	81 - 137
12	X-RAY DIFFRACTION	12	E	138 - 217
13	X-RAY DIFFRACTION	13	F	1 - 105
14	X-RAY DIFFRACTION	14	F	106 - 188
15	X-RAY DIFFRACTION	15	F	189 - 211
16	X-RAY DIFFRACTION	16	G	1 - 80
17	X-RAY DIFFRACTION	17	G	81 - 172
18	X-RAY DIFFRACTION	18	G	173 - 216

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