PDB-6b4o: 1.73 Angstrom Resolution Crystal Structure of Glutathione Reducta...

ID or keywords:

Entry

Database: PDB / ID: 6b4o

Title

1.73 Angstrom Resolution Crystal Structure of Glutathione Reductase from Enterococcus faecalis in Complex with FAD

Components

Glutathione reductase

Keywords

HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Glutathione Reductase / FAD

Function / homology

Function and homology information

glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / NADP binding / cellular response to oxidative stress / metal ion binding / cytosol
Similarity search - Function

Biological species

Enterococcus faecalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Minasov, G. / Warwzak, Z. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.73 Angstrom Resolution Crystal Structure of Glutathione Reductase from Enterococcus faecalis in Complex with FAD.
Authors: Minasov, G. / Warwzak, Z. / Shuvalova, L. / Dubrovska, I. / Cardona-Correa, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics ...

History

Deposition	Sep 27, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 11, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6b4o.cif.gz	767.5 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b4/6b4o ftp://data.pdbj.org/pub/pdb/validation_reports/b4/6b4o	HTTPS FTP

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Related structure data

Related structure data	5v36S S: Starting model for refinement
Similar structure data	5u1o-1 5v36-d 6du7-2 5x1y-2 6du7-4 4dna-d 4pjl-d 2wov-1 5grt-1 5u1o-2 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
Other databases	TargetTrack: CSGID-IDP07317

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (8) #154 - Oct 2012 Citric Acid Cycle similarity (8) #82 - Oct 2006 Cytochrome p450 similarity (2)

Deposited unit

A: Glutathione reductase

B: Glutathione reductase

C: Glutathione reductase

D: Glutathione reductase

hetero molecules

203 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glutathione reductase

B: Glutathione reductase

hetero molecules

defined by author&software
Evidence: homology, 5V36
101 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glutathione reductase

D: Glutathione reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	61.686, 152.613, 98.531
Angle α, β, γ (deg.)	90.00, 94.97, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glutathione reductase Mass: 49693.117 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (strain ATCC 700802 / V583) (bacteria) Strain: V583 / Gene: gor / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic References: UniProt: Q82Z09, adenosylhomocysteinase, glutathione-disulfide reductase
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1916 / Source method: isolated from a natural source / Formula: H₂O
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: 2.27 Å³/Da / Density % sol: 45.9 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 12.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD, 1mM NADH; Screen: JCSG+ (H11), 0.2M Magnesium chloride, 0.1M Bis-Tris (pH 5.5), 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2017 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.73→30 Å / Num. obs: 188943 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 24.5 Å² / R_merge(I) obs: 0.059 / R_pim(I) all: 0.032 / R_sym value: 0.059 / Χ²: 1.002 / Net I/σ(I): 22.1
Reflection shell	Resolution: 1.73→1.76 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.722 / Mean I/σ(I) obs: 2 / Num. unique obs: 9415 / CC_1/2: 0.739 / R_pim(I) all: 0.4 / R_sym value: 0.722 / Χ²: 1.029 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5V36

5v36

Resolution: 1.73→29.98 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.959 / SU B: 5.242 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19478	9443	5 %	RANDOM
R_work	0.1624	-	-	-
obs	0.164	178985	99.97 %	-

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: 29.547 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.99 Å²	0 Å²	-0.43 Å²
2-	-	-0.66 Å²	0 Å²
3-	-	-	-0.25 Å²

Refinement step

Cycle: 1 / Resolution: 1.73→29.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13890	0	243	1916	16049

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	14962
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	13598
X-RAY DIFFRACTION	r_angle_refined_deg	1.447	1.97	20336
X-RAY DIFFRACTION	r_angle_other_deg	0.873	3	31649
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.011	5	1911
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.857	24.841	690
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.533	15	2538
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.6	15	74
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	2196
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.02	17063
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	3023
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	0.757	1.436	7486
X-RAY DIFFRACTION	r_mcbond_other	0.757	1.435	7485
X-RAY DIFFRACTION	r_mcangle_it	1.259	2.148	9448
X-RAY DIFFRACTION	r_mcangle_other	1.259	2.148	9449
X-RAY DIFFRACTION	r_scbond_it	1.214	1.659	7476
X-RAY DIFFRACTION	r_scbond_other	1.214	1.659	7477
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.939	2.418	10888
X-RAY DIFFRACTION	r_long_range_B_refined	5.496	19.175	17772
X-RAY DIFFRACTION	r_long_range_B_other	5.244	17.937	17204
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.73→1.775 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.297	704	-
R_work	0.265	13188	-
obs	-	-	99.99 %

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	1.4584	0.8188	-0.4225	0.6871	-0.2786	0.262	0.1334	-0.103	-0.0515	0.1051	-0.081	0.0786	0.0673	0.0079	-0.0524	0.1503	-0.0453	-0.0114	0.0271	0.0043	0.1338	-20.7212	73.1687	102.6852
2	1.2336	0.214	0.1149	0.6186	-0.0266	0.2041	0.1437	-0.1188	-0.1466	0.1503	-0.0934	0.0155	0.1095	-0.0073	-0.0503	0.188	-0.0517	-0.0364	0.0278	0.0261	0.1267	-15.8802	66.3686	108.2108
3	1.5006	0.5428	1.0401	1.297	-0.1438	2.6433	0.277	-0.0118	-0.2918	0.0481	-0.0831	-0.2137	0.3714	0.1728	-0.1939	0.202	0.0353	-0.0886	0.0212	0.0022	0.2708	1.4163	56.5323	102.2695
4	1.5085	0.4864	-0.3374	0.8948	-0.0762	0.4278	0.1143	0.0619	-0.1786	0.039	-0.0285	0.0895	0.1317	-0.0467	-0.0858	0.1855	-0.0436	-0.0595	0.0229	0.0078	0.1897	-28.8841	59.5733	96.3944
5	3.6763	3.5174	1.5141	6.1814	1.7692	1.6858	0.0124	0.1361	-0.4176	-0.1683	0.1027	-0.3261	0.2028	0.0517	-0.1151	0.1506	0.0522	-0.0262	0.047	-0.0607	0.1157	-5.3309	62.0072	77.6078
6	0.8276	0.0432	0.225	1.6971	-0.3798	0.8285	0.0138	0.1076	-0.1315	-0.2455	0.0611	-0.0234	0.1954	-0.0369	-0.0749	0.1667	0.0015	-0.0194	0.0392	-0.0489	0.112	-11.5719	68.5929	75.7661
7	0.3409	-0.0113	0.2374	0.3434	0.0755	2.1798	0.0522	0.1006	-0.0177	-0.088	0.0142	-0.0907	0.1101	0.1951	-0.0664	0.1077	0.0181	0.0111	0.0409	-0.0262	0.0966	4.8914	85.497	67.0049
8	0.4781	-0.2816	0.2667	1.2872	-0.3386	0.9721	-0.0487	0.0118	0.0436	-0.0254	0.0437	-0.0587	-0.1603	-0.0263	0.005	0.137	0.0215	-0.0153	0.0389	-0.0265	0.0827	-1.579	103.2716	78.8013
9	1.1276	0.8128	-0.1195	2.4195	-0.4514	1.0739	-0.0235	0.022	0.0458	0.1777	0.0472	0.0306	-0.1973	-0.1346	-0.0238	0.1672	0.0663	-0.0169	0.0358	-0.0181	0.0693	-7.3054	106.8321	82.0607
10	0.5518	-0.1016	-0.2423	0.3923	-0.2787	1.7178	0.0127	0.0817	0.0197	-0.1093	0.0154	0.0588	0.0277	-0.1872	-0.0282	0.1323	0.0007	-0.023	0.0491	-0.0232	0.0861	-10.8135	87.4345	59.3503
11	5.062	-0.1375	5.1941	1.0911	-0.2289	6.0948	-0.0991	-0.2462	0.111	0.0619	-0.0207	0.1744	-0.1617	-0.452	0.1198	0.0123	0.021	0.0195	0.0693	-0.0013	0.0976	-24.836	87.4625	86.3464
12	1.0729	0.184	0.4696	1.4141	-0.2298	1.5211	0.0368	-0.0073	-0.0689	-0.0092	0.0769	0.1697	0.0996	-0.2594	-0.1137	0.0895	-0.0016	-0.0084	0.0806	0.0057	0.1158	-23.2668	79.4997	82.4363
13	0.5447	-0.311	0.9219	0.7048	-0.789	1.7512	0.0122	0.1435	0.0182	-0.2304	-0.1667	-0.1041	0.1856	0.2964	0.1545	0.2045	0.0736	0.0886	0.1155	0.0386	0.1252	13.6551	39.941	43.8713
14	2.0962	-0.2577	1.0376	1.4077	-0.6877	2.1309	-0.0757	0.2335	0.2388	-0.2845	-0.218	-0.2747	-0.1142	0.3786	0.2937	0.189	0.0194	0.0961	0.0794	0.0807	0.1196	13.35	50.527	39.5505
15	1.3752	-1.4502	0.3256	2.4829	-0.8068	2.3534	-0.0713	0.2761	0.5462	-0.1534	-0.4335	-1.0347	-0.4415	0.9162	0.5049	0.2231	-0.1809	0.0522	0.3771	0.2566	0.6261	28.6013	58.5292	47.4612
16	0.5272	-0.0273	0.5829	1.4292	-0.6397	2.0121	-0.0863	-0.0877	0.1051	0.0161	-0.0131	-0.0457	-0.3148	-0.1501	0.0993	0.1793	0.0717	0.0018	0.0362	-0.0182	0.0766	-0.1375	54.834	50.1358
17	5.0095	-4.9204	-2.1689	7.0335	1.3132	1.6305	-0.1542	-0.2072	0.4286	0.1146	0.0899	-0.5293	-0.2184	0.2829	0.0643	0.2696	-0.0592	-0.1883	0.1661	-0.0022	0.2675	21.1235	52.2484	71.9181
18	1.3334	-1.0147	0.4114	1.6101	-0.8821	1.3319	-0.2569	-0.0287	0.2807	0.3226	0.0175	-0.3054	-0.3162	0.0417	0.2394	0.1748	0.0348	-0.0755	0.0302	-0.0187	0.1485	14.1489	46.1419	72.4437
19	0.1417	-0.2195	0.0971	0.3982	-0.2475	2.1803	0.0342	0.1056	0.0897	-0.0435	-0.1537	-0.195	-0.0381	0.3118	0.1195	0.0823	0.0227	0.0221	0.1139	0.0513	0.1659	26.5976	30.4176	80.1731
20	0.2814	-0.2593	0.0927	0.7314	-0.0238	1.6381	0.0358	0.0404	0.0596	0.0253	-0.1366	-0.1944	-0.1032	0.2916	0.1008	0.0719	0.0005	0.0041	0.0989	0.0458	0.1935	30.4324	28.0687	88.5294
21	0.4372	0.263	-0.3186	2.1598	-0.9099	1.3676	0.0268	0.0946	-0.1308	-0.2465	-0.2115	-0.3269	0.3211	0.1973	0.1847	0.1948	0.1128	0.0862	0.1052	-0.0024	0.1732	24.3095	11.3229	71.4054
22	1.7234	-1.1685	0.0442	3.2188	-1.344	1.8649	0.0534	0.141	-0.1267	-0.4992	-0.1733	-0.1847	0.4813	0.1177	0.1199	0.2656	0.0728	0.0875	0.0762	-0.0487	0.1311	19.119	7.8289	67.4577
23	0.3113	-0.0807	0.4129	0.4285	-0.4836	1.3193	-0.0068	0.0159	0.0279	-0.0292	-0.0371	-0.0329	0.04	-0.1215	0.0438	0.1128	0.027	0.0144	0.0886	-0.0148	0.1529	9.7112	27.3832	82.2782
24	0.7786	-0.1708	0.1056	1.717	-0.7021	1.5936	-0.0383	0.0578	0.0839	-0.0595	0.0662	0.041	-0.0153	-0.0822	-0.0278	0.1122	0.038	0.0092	0.0723	-0.0058	0.0821	3.673	35.2916	63.9202

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 74
2	X-RAY DIFFRACTION	2	A	75 - 200
3	X-RAY DIFFRACTION	3	A	201 - 258
4	X-RAY DIFFRACTION	4	A	259 - 352
5	X-RAY DIFFRACTION	5	A	353 - 384
6	X-RAY DIFFRACTION	6	A	385 - 449
7	X-RAY DIFFRACTION	7	B	2 - 142
8	X-RAY DIFFRACTION	8	B	143 - 200
9	X-RAY DIFFRACTION	9	B	201 - 260
10	X-RAY DIFFRACTION	10	B	261 - 357
11	X-RAY DIFFRACTION	11	B	358 - 384
12	X-RAY DIFFRACTION	12	B	385 - 449
13	X-RAY DIFFRACTION	13	C	1 - 89
14	X-RAY DIFFRACTION	14	C	90 - 200
15	X-RAY DIFFRACTION	15	C	201 - 267
16	X-RAY DIFFRACTION	16	C	268 - 354
17	X-RAY DIFFRACTION	17	C	355 - 384
18	X-RAY DIFFRACTION	18	C	385 - 449
19	X-RAY DIFFRACTION	19	D	0 - 74
20	X-RAY DIFFRACTION	20	D	75 - 142
21	X-RAY DIFFRACTION	21	D	143 - 200
22	X-RAY DIFFRACTION	22	D	201 - 261
23	X-RAY DIFFRACTION	23	D	262 - 384
24	X-RAY DIFFRACTION	24	D	385 - 449

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