PDB-2w8m: Structure of D212, a nuclease from a fusselovirus.

ID or keywords:

Entry

Database: PDB / ID: 2w8m

Title

Structure of D212, a nuclease from a fusselovirus.

Components

ORF D212

Keywords

HYDROLASE / SSV1 / CRENARCHAEAL VIRUS

Function / homology

D212 PD-(D/E)XK nuclease, catalytic motif / D212, catalytic domain / D212, catalytic domain superfamily / Viral/Archaeal nuclease / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / ORF D212

Function and homology information

Biological species

SULFOLOBUS VIRUS RAGGED HILLS

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2.4 Å

Authors

Menon, S.K. / Young, M.J. / Lawrence, C.M.

Citation

Journal: J. Virol. / Year: 2010
Title: The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.
Authors: Menon, S.K. / Eilers, B.J. / Young, M.J. / Lawrence, C.M.

History

Deposition	Jan 17, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 3, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Jun 13, 2018	Group: Advisory / Data collection / Database references Category: citation / diffrn_radiation / pdbx_unobs_or_zero_occ_atoms Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.3	May 8, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	2w8m_validation.pdf.gz	434.3 KB	Display	wwPDB validaton report
Full document	2w8m_full_validation.pdf.gz	437.5 KB	Display
Data in XML	2w8m_validation.xml.gz	14.2 KB	Display
Data in CIF	2w8m_validation.cif.gz	19 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w8/2w8m ftp://data.pdbj.org/pub/pdb/validation_reports/w8/2w8m	HTTPS FTP

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Related structure data

Similar structure data	6r0m-d 1te1-d 4b28-d 2g5d-d 3nvr-d 6qci-d 2g6g-d 3kv0-2 2zwr-d 2iiq-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ORF D212

B: ORF D212

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.477, 81.971, 60.160
Angle α, β, γ (deg.)	90.00, 115.40, 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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	19 - 55
2	1	1	5	B	19 - 55
1	2	1	5	A	66 - 107
2	2	1	5	B	66 - 107
1	3	1	5	A	112 - 169
2	3	1	5	B	112 - 169
1	4	1	3	A	176 - 207
2	4	1	3	B	176 - 207

NCS oper: (Code: given
Matrix: (0.321, -0.155, -0.934), (-0.155, -0.982, 0.11), (-0.934, 0.11, -0.34)
Vector: 81.43211, 120.39913, 95.18207)

#1: Protein	ORF D212 / D212 Mass: 25106.721 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS VIRUS RAGGED HILLS / Plasmid: PEXP14-SSVRH D212 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6TRV5
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal	Density Matthews: 2.42 Å³/Da / Density % sol: 49.14 % Description: MAD PHASE FROM THE INCORPORATED PT WAS COMBINED WITH MIR PHASES FROM BR AND PT DERIVATIVES.
Crystal grow	pH: 7.5 Details: 0.1 M HEPES (PH 7.5), 0.05 M K2HPO4, 10% (W/V) PEG 8000 WITH 25% GYLCEROL AS CRYOPROTECTANT

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SSRL	BL9-2	1	0.85, 2.06
SYNCHROTRON	SSRL	BL9-1	2	0.77, 0.98

Detector

Type	ID	Detector	Date
MARMOSAIC 325 mm CCD	1	CCD	Jan 21, 2008
ADSC CCD	2	CCD

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.85	1
2	2.06	1
3	0.77	1
4	0.98	1

Reflection

Resolution: 2.4→30 Å / Num. obs: 17143 / % possible obs: 92.9 % / Observed criterion σ(I): 5 / Redundancy: 3.1 % / R_merge(I) obs: 0.03 / Net I/σ(I): 32

Reflection shell

Resolution: 2.4→2.49 Å / Redundancy: 3 % / R_merge(I) obs: 0.33 / Mean I/σ(I) obs: 4.3 / % possible all: 95.7

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SOLVE		phasing
RESOLVE		phasing
REFMAC	5.2.0019	refinement

Refinement

Method to determine structure:

MIRAS
Starting model: NONE

Resolution: 2.4→29.1 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.914 / SU B: 14.435 / SU ML: 0.169 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.375 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 57-67,108-112,170-175,208-212 IN CHAIN A AND 61- 68,100-106,172-174,205-212 IN CHAIN B ARE DISORDERED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.245	914	5.1 %	RANDOM
R_work	0.209	-	-	-
obs	0.211	17143	94.1 %	-

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: 32.21 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	-0.04 Å²
2-	-	0.87 Å²	0 Å²
3-	-	-	-0.89 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→29.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2811	0	0	75	2886

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	2875
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2023
X-RAY DIFFRACTION	r_angle_refined_deg	0.698	1.984	3874
X-RAY DIFFRACTION	r_angle_other_deg	2.096	3	4908
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.531	5	327
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.693	23.359	131
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.344	15	545
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.528	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.043	0.2	424
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	3048
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	617
X-RAY DIFFRACTION	r_nbd_refined	0.175	0.2	536
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	1779
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1367
X-RAY DIFFRACTION	r_nbtor_other	0.078	0.2	1381
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.113	0.2	84
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	0.216	0.2	15
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.153	0.2	47
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.334	0.2	15
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	1.261	1.5	2206
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.239	2	2661
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.331	3	1715
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.842	4.5	1212
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

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

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	172	tight positional	0.02	0.05
2	B	172	tight positional	0.02	0.05
1	A	744	medium positional	0.43	0.5
2	B	744	medium positional	0.43	0.5
1	A	1302	loose positional	0.77	5
2	B	1302	loose positional	0.77	5
1	A	172	tight thermal	0.02	0.5
2	B	172	tight thermal	0.02	0.5
1	A	744	medium thermal	0.17	2
2	B	744	medium thermal	0.17	2
1	A	1302	loose thermal	1.01	10
2	B	1302	loose thermal	1.01	10

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.299	66
R_work	0.238	1275

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	9.8907	6.7877	12.9707	13.9315	2.7099	21.1439	0.446	-0.2108	0.4618	0.9534	-0.04	-0.2951	0.764	-0.5162	-0.406	0.3929	-0.0347	-0.1048	0.2641	-0.0277	0.4441	50.0495	56.6232	53.1191
2	7.3137	2.206	9.1397	3.3023	0.8006	16.3846	-0.1442	-0.0036	0.4447	-0.3306	0.0413	-0.0596	-0.4298	0.1004	0.103	0.2808	-0.0316	-0.0158	0.186	-0.0273	0.1817	42.5427	56.4437	36.3708
3	15.6974	4.6334	-14.7826	3.2325	-1.2429	19.1425	-0.4119	0.2135	0.3203	-0.3062	-0.2466	0.3422	-0.5501	0.4592	0.6585	0.1616	0.0919	-0.135	0.2166	0.0355	0.1673	31.3923	54.2258	32.0263
4	23.5909	-1.3083	3.4577	0.7543	1.4005	4.2257	-0.4064	-0.129	1.1943	0.1117	0.2004	0.6448	-0.292	-0.4445	0.2061	0.2937	0.0095	0.0456	0.3784	0.0465	0.2883	23.8345	44.5034	45.1543
5	4.8618	-1.4669	2.0101	11.6382	-3.9886	9.483	-0.1805	-0.4542	0.2149	-0.1629	0.4329	0.9775	-0.3394	-1.2	-0.2524	0.2065	0.0601	0.0536	0.3686	-0.0304	0.2987	27.8709	50.1643	39.9941
6	0.3817	-1.1171	-0.3006	3.2695	0.8799	0.2368	-0.0301	-0.1538	0.4983	0.4513	-0.1417	-0.3216	0.1952	0.1724	0.1718	0.3417	0.0259	0.0323	0.4535	0.0626	0.3195	45.4107	45.6289	45.2913
7	30.7911	-16.6327	-13.3809	11.4363	2.6988	22.5556	-0.8049	-1.2714	1.9542	0.9259	0.5819	-1.5691	-1.5333	1.8241	0.2231	0.342	-0.0417	-0.1284	0.4352	0.1184	0.5911	59.2493	43.0437	44.8601
8	33.999	4.4721	8.2445	4.1512	0.0419	2.5138	-0.5226	-0.9414	-0.8331	0.2717	0.2589	-0.0843	0.311	0.1023	0.2637	0.2163	0.0333	0.0837	0.2903	0.054	0.165	38.4038	36.2931	47.4709
9	2.2047	0.6864	0.2045	2.5295	-0.4579	2.5989	-0.262	0.392	-0.0791	-0.2472	0.1379	0.0791	0.0783	-0.0971	0.1241	0.243	-0.0172	0.0651	0.2359	-0.0112	0.2086	38.7209	42.1538	39.8058
10	27.8841	9.8899	5.4853	32.0018	-2.1109	25.9371	-0.2032	1.8376	-2.2569	-1.4053	0.6382	-2.6465	-0.9544	2.7574	-0.435	0.268	-0.178	0.191	0.5071	-0.1354	0.5767	54.8121	50.6412	35.0905
11	10.593	2.2244	-0.627	13.2813	-8.2844	5.2242	-0.2887	0.3219	-0.5012	-0.6655	0.2567	0.2437	0.3524	-0.1437	0.0319	0.2416	0.0091	0.0969	0.2232	-0.0509	0.1691	43.8517	36.1601	37.3984
12	18.6053	3.8016	-0.4732	9.1634	13.8001	40.4617	0.5998	-0.3606	-1.0362	0.6599	0.2213	-0.0227	1.6289	-0.6336	-0.8212	0.3444	0.1671	0.1959	0.0946	0.1342	0.4914	47.9351	28.4485	43.6163
13	13.1438	3.4536	-6.3827	8.5406	-7.8104	22.577	-0.3347	-0.5827	-0.4798	0.0332	-0.1246	0.0114	0.4127	1.4499	0.4593	0.1093	0.0733	0.0619	0.115	0.0324	0.2043	49.7993	37.4947	42.2475
14	29.0053	3.412	4.5275	13.6744	-3.3769	8.574	0.4126	-0.5258	0.3026	-1.056	-0.6216	-0.475	-0.2386	0.152	0.209	0.2009	-0.0388	0.0741	0.168	-0.0205	0.035	40.5808	45.8651	29.6538
15	2.1374	6.0129	-2.773	18.962	-3.6119	12.1735	0.4045	0.4334	0.14	0.2568	-0.2876	1.9086	0.0853	-1.8605	-0.1169	0.2383	-0.0391	-0.0409	0.5739	-0.09	0.2601	25.2373	44.3878	29.1993
16	46.5054	14.4019	-15.6453	20.2396	-10.5695	7.34	0.4394	-3.3238	2.6219	1.583	-0.3978	1.4318	-0.8829	1.0536	-0.0416	0.8727	0.0488	0.005	0.6671	-0.1654	0.5432	29.5275	59.8065	39.6527
17	33.8881	0.5605	36.1226	10.4278	3.7387	39.4516	-0.6682	0.8534	1.0331	-0.8807	0.1387	-0.4699	-0.5728	-0.4782	0.5296	0.3979	0.0132	-0.0701	0.2157	-0.0024	0.3633	42.5234	64.5617	37.798
18	5.1809	3.8393	4.2184	5.4498	2.4941	8.9756	0.3024	0.1566	-0.2219	0.0899	-0.3577	-0.5344	0.7357	0.2408	0.0553	0.2148	0.037	-0.0453	0.1514	-0.0043	0.2964	55.1534	62.0002	51.4322
19	9.3847	-2.5066	-2.5053	12.1709	3.3517	1.355	0.0446	0.3542	-0.6561	-0.3577	-0.2479	0.7846	0.0733	-0.6745	0.2033	0.337	-0.071	-0.0624	0.3475	0.0847	0.1783	45.1999	67.1673	59.1395
20	0.4713	-0.1767	-0.831	3.4593	0.9317	1.5783	-0.1032	0.2443	0.0258	0.4117	0.016	0.4599	0.1623	-0.6377	0.0872	0.2339	-0.0381	0.0607	0.389	0.0011	0.2329	42.3324	74.117	56.2091
21	9.096	-0.7376	1.3322	5.7262	2.8497	8.9692	-0.083	-1.1961	-0.0813	0.7776	-0.1132	0.1909	1.2504	-0.1775	0.1961	0.373	-0.0555	0.0921	0.4206	-0.0265	0.232	46.7674	71.1548	61.1376
22	0.6537	-0.3122	4.1742	6.8144	-11.859	41.2571	-0.9038	-0.5825	-0.7382	-0.5244	0.7708	0.6802	1.9352	-0.7844	0.133	0.5626	0.0926	0.1024	0.5732	0.1135	0.5604	50.6778	74.2286	28.3758
23	4.3158	-0.8752	-4.5343	4.9639	2.0761	14.9903	0.2224	0.324	0.5223	-0.3909	0.1565	0.0715	-0.2198	-0.5851	-0.3789	0.1705	0.0277	-0.0295	0.2492	0.0515	0.206	46.6425	82.6608	44.5208
24	4.5033	0.5595	-0.5315	7.1533	5.5315	11.3656	-0.3503	0.3425	-0.2019	-0.0859	0.4021	-0.5556	0.5741	0.8573	-0.0519	0.2554	0	0.108	0.3095	0.0079	0.22	53.1146	73.3566	44.8364
25	4.9861	3.1068	2.2742	2.7489	-0.687	6.4815	-0.1567	0.2888	-0.0918	0.5077	0.2057	-0.7024	0.1701	0.4776	-0.049	0.1761	-0.0187	0.0581	0.2726	0.0328	0.1526	55.8483	77.7334	44.8152
26	19.3277	-5.0787	-1.2626	38.71	13.4151	9.5696	-0.2832	-0.5037	0.6805	0.9316	0.4496	-0.0609	-1.097	0.4902	-0.1664	0.2806	-0.116	0.0228	0.251	0.1456	0.1995	56.6692	90.6952	41.5447
27	19.0784	-7.9437	2.8958	6.8025	-2.1552	16.47	0.3948	1.153	-0.091	-0.0924	-0.0459	0.9612	-0.968	-2.3841	-0.3489	0.3335	0.1039	-0.0044	0.4023	0.1778	0.2268	42.7871	87.8078	35.019
28	5.2785	2.3756	-1.4981	9.1787	-1.8372	9.5624	0.0866	0.2316	0.0198	-0.988	0.0292	-0.4247	-0.4189	0.3998	-0.1158	0.2085	-0.0487	0.0073	0.1718	0.0072	0.0426	53.4446	80.5524	39.1297
29	6.5741	-8.6273	-9.792	11.3328	12.032	75.3404	0.0919	0.1321	-0.2529	0.685	-0.127	-0.7807	0.8641	1.7176	0.0351	0.0935	-0.0344	-0.0607	0.2362	0.0657	0.3005	59.8183	72.2143	54.351
30	14.6408	-17.2132	14.4837	34.2999	-11.1245	16.807	-0.8718	-1.8932	0.2414	3.0001	0.8315	0.1932	0.1162	-0.9838	0.0403	0.428	-0.0658	-0.1024	0.4189	0.0064	0.154	54.7816	76.0399	67.5176

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 27
2	X-RAY DIFFRACTION	2	A	28 - 43
3	X-RAY DIFFRACTION	3	A	44 - 54
4	X-RAY DIFFRACTION	4	A	68 - 75
5	X-RAY DIFFRACTION	5	A	76 - 94
6	X-RAY DIFFRACTION	6	A	95 - 103
7	X-RAY DIFFRACTION	7	A	104 - 117
8	X-RAY DIFFRACTION	8	A	118 - 129
9	X-RAY DIFFRACTION	9	A	130 - 141
10	X-RAY DIFFRACTION	10	A	142 - 148
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12	X-RAY DIFFRACTION	12	A	160 - 169
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16	X-RAY DIFFRACTION	16	B	17 - 21
17	X-RAY DIFFRACTION	17	B	22 - 28
18	X-RAY DIFFRACTION	18	B	29 - 48
19	X-RAY DIFFRACTION	19	B	49 - 70
20	X-RAY DIFFRACTION	20	B	71 - 84
21	X-RAY DIFFRACTION	21	B	85 - 98
22	X-RAY DIFFRACTION	22	B	99 - 112
23	X-RAY DIFFRACTION	23	B	113 - 131
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25	X-RAY DIFFRACTION	25	B	146 - 158
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27	X-RAY DIFFRACTION	27	B	165 - 176
28	X-RAY DIFFRACTION	28	B	177 - 188
29	X-RAY DIFFRACTION	29	B	189 - 198
30	X-RAY DIFFRACTION	30	B	199 - 204

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