PDB-2gcj: Crystal Structure of the Pob3 middle domain

ID or keywords:

Entry

Database: PDB / ID: 2gcj

Title

Crystal Structure of the Pob3 middle domain

Components

Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

Keywords

REPLICATION / Chromatin / FACT / double PH domain

Function / homology

Function and homology information

Regulation of TP53 Activity through Phosphorylation / FACT complex / regulation of chromatin organization / nucleosome organization / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA-templated DNA replication / chromatin organization / DNA repair ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

VanDemark, A.P.

Citation

Journal: Mol.Cell / Year: 2006
Title: The Structure of the yFACT Pob3-M Domain, Its Interaction with the DNA Replication Factor RPA, and a Potential Role in Nucleosome Deposition.
Authors: VanDemark, A.P. / Blanksma, M. / Ferris, E. / Heroux, A. / Hill, C.P. / Formosa, T.

History

Deposition	Mar 14, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 23, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 20, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Feb 14, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2gcj.cif.gz	391.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2gcj.ent.gz	324.5 KB	Display	PDB format
PDBx/mmJSON format	2gcj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2gcj_validation.pdf.gz	458.4 KB	Display	wwPDB validaton report
Full document	2gcj_full_validation.pdf.gz	485.4 KB	Display
Data in XML	2gcj_validation.xml.gz	36.2 KB	Display
Data in CIF	2gcj_validation.cif.gz	49 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gc/2gcj ftp://data.pdbj.org/pub/pdb/validation_reports/gc/2gcj	HTTPS FTP

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Related structure data

Related structure data	2gclC C: citing same article (ref.)
Similar structure data	3rig-1 4xpm-d 2gcl-1 4f56-2 3vkx-d 2qms-4 3rig-2 6m72-d 6lf2-d 5ojo-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) 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

Related structure data

2gclC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (1) #40 - Apr 2003 RNA Polymerase similarity (2) #255 - Mar 2021 Cisplatin and DNA similarity (2) #67 - Jul 2005 TATA-Binding Protein similarity (1) #245 - May 2020 Spliceosomes similarity (1)

Deposited unit

A: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

B: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

C: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

D: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

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

1

A: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

defined by author
30.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

defined by author
30.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

defined by author
30.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

defined by author
30.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	57.868, 157.527, 57.787
Angle α, β, γ (deg.)	90.00, 89.77, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Biological Unit is the monomer.

#1: Protein	Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region Mass: 30341.287 Da / Num. of mol.: 4 / Fragment: Pob3 Middle domain / Mutation: Q308K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: Pob3 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: Q04636
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Hypothetical 63.0 kDa protein in DAK1-ORC1 intergenic region

Mass: 30341.287 Da / Num. of mol.: 4 / Fragment: Pob3 Middle domain / Mutation: Q308K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (brewer's yeast)
Gene: Pob3 / Plasmid: PET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 Codon+ / References: UniProt: Q04636

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.31 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 21% PEG 3350, 20% Glycerol, 200mM NaCl, 50mM Ammonium Sulphate, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2005
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.49→78 Å / Num. all: 34206 / Num. obs: 31162 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell	Resolution: 2.49→2.59 Å / % possible all: 92.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
ADSC		data collection
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Wild-type protein

Resolution: 2.55→78.81 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.902 / SU B: 30.97 / SU ML: 0.317 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30287	1542	5 %	RANDOM
R_work	0.21472	-	-	-
obs	0.21926	29326	91.66 %	-
all	-	34206	-	-

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: 10.237 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.41 Å²	0 Å²	1 Å²
2-	-	-0.44 Å²	0 Å²
3-	-	-	-1.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→78.81 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7569	0	0	80	7649

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	7689
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.504	1.968	10385
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.105	5	912
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.947	24.145	386
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.123	15	1400
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.663	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1158
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5791
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	3215
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.32	0.2	5087
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	275
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	0.175	0.2	106
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.219	0.2	24
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	0.442	1.5	4690
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.791	2	7472
X-RAY DIFFRACTION	r_scbond_it	1.347	3	3311
X-RAY DIFFRACTION	r_scangle_it	2.068	4.5	2913
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.55→2.616 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.419	122	-
R_work	0.315	2204	-
obs	-	-	92.74 %

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	9.4869	-5.2036	-4.3807	13.4711	6.5179	12.3891	0.3695	1.0347	0.4094	-0.5146	-0.0719	-1.1573	-0.2312	0.9934	-0.2976	0.1292	-0.0095	-0.0116	0.4034	-0.0498	-0.0452	33.5191	1.2606	13.1684
2	8.6527	-2.1588	-5.005	6.7672	2.2001	12.6548	0.586	0.0554	-0.1458	-0.8655	-0.3486	-0.0738	-0.6037	-0.5975	-0.2374	0.2393	0.0567	-0.136	0.1831	0.0312	-0.034	25.6511	1.7566	8.9035
3	4.7802	-1.6979	0.9064	9.6253	4.9212	11.7359	0.2115	0.3186	0.0296	-0.4634	-0.0086	0.2147	0.2754	0.0866	-0.2029	0.0604	-0.0127	-0.0429	0.0554	0.0624	0.0181	27.0947	-0.4388	18.9125
4	7.8855	-2.4426	1.0332	10.5674	-1.6286	2.7593	0.2601	-0.1609	-0.3878	0.7292	-0.0061	0.538	-0.2153	-0.2935	-0.254	0.1117	0.006	-0.0741	0.1939	0.0137	-0.0382	23.9722	2.7709	24.7717
5	8.9662	-1.8632	-2.6284	7.8198	4.1311	11.5401	-0.166	-0.3625	-0.1838	0.2769	0.4498	-0.2215	0.0427	0.9645	-0.2838	0.3756	0.0141	-0.0631	-0.0014	-0.0562	0.3145	29.7142	-20.545	26.6687
6	9.8912	6.2636	-1.6802	12.3437	0.0496	13.1421	0.4232	0.3133	-0.8877	0.2585	-0.6984	0.9117	-0.4762	0.5253	0.2753	0.3188	0.1167	-0.2155	0.083	-0.1072	0.4187	23.29	-24.3216	20.4866
7	4.3783	-0.0455	1.085	10.2455	5.1888	9.4567	-0.1147	-0.1377	-0.9021	0.9404	0.0831	0.5622	0.804	0.1061	0.0316	0.4664	0.1258	-0.0406	-0.0014	-0.0382	0.4451	23.799	-30.0267	26.4756
8	13.3082	-8.9263	6.1523	18.0252	-9.2321	5.0095	0.3164	0.5144	-0.6223	-0.7751	-0.1895	1.1557	0.5873	-0.3811	-0.1268	0.1689	-0.0578	-0.0721	0.1524	-0.0527	-0.1006	25.104	11.0567	-15.5218
9	1.4659	0.9183	0.6136	4.3104	0.7291	6.8111	-0.1383	0.2758	0.0805	-0.4412	-0.0204	-0.0384	0.3305	0.3987	0.1587	-0.0352	0.0253	-0.1085	0.0847	0.0176	0.0343	31.5408	14.6876	-16.5077
10	5.3128	-2.5144	-0.2212	11.0057	-3.3016	5.7036	-0.2532	0.1465	-0.1713	-0.0936	0.001	-0.0878	0.5381	0.1797	0.2522	0.0513	-0.0146	-0.0819	0.019	-0.0765	-0.0495	31.9511	12.6602	-10.3322
11	9.1549	-5.1569	-2.6111	5.4281	-1.2474	6.5433	0.048	-0.3267	0.5061	0.5224	0.0134	-0.1461	0.169	0.4481	-0.0614	0.034	0.0599	-0.0513	-0.0027	-0.0286	0.0318	34.1916	10.3717	-4.3963
12	5.9894	-11.6412	0.4761	22.7313	-0.8278	0.1286	-0.874	-0.9522	-0.9168	2.6377	1.2028	1.2317	-0.3694	-0.7177	-0.3289	0.432	0.1749	0.0737	0.3139	0.0954	0.2751	28.4529	30.4816	4.4117
13	11.4391	0.6782	1.3018	9.188	-5.3359	6.6992	-0.2345	-0.1121	0.9015	-0.0984	0.397	0.3955	0.0347	-0.9473	-0.1625	0.1707	0.1118	-0.0583	-0.0324	-0.0966	0.07	27.4811	35.2688	-6.2587
14	8.6046	-5.8128	1.0894	9.0471	-1.3886	10.8248	0.397	-0.1491	0.4169	-0.2242	-0.1976	-0.6864	-0.1686	-0.422	-0.1994	0.06	-0.0035	-0.1005	-0.0317	0.0251	0.2321	33.9396	36.9871	-7.4499
15	5.9159	-0.8989	2.2308	7.2448	-5.4624	8.0257	-0.5267	-0.2238	0.9044	1.3855	0.0332	-0.7708	-1.1083	-0.3007	0.4935	0.2939	0.0475	-0.2359	-0.0035	-0.1039	0.4337	33.2663	43.3238	-1.6941
16	7.6939	6.8171	-5.9045	11.5661	-6.4927	12.108	-0.0518	-0.0911	0.6063	0.8134	0.2428	1.0481	-0.8018	-0.6767	-0.191	0.038	0.1121	-0.0592	0.1031	0.0402	0.036	-3.9206	17.2613	-12.5828
17	5.4448	0.3588	-3.5914	1.1558	-1.2731	7.7987	-0.0093	-0.2644	0.0882	0.8339	-0.0842	-0.0631	-0.3851	0.5355	0.0935	0.0599	-0.0158	-0.1331	0.1537	-0.0136	0.0425	4.4025	15.6719	-9.4316
18	3.9976	1.7571	-0.8924	11.2534	-2.4737	5.6525	-0.176	-0.0425	0.2569	0.0934	0.0073	-0.1923	-0.4679	0.1381	0.1686	-0.0665	0.0368	-0.0885	0.0501	-0.0224	-0.016	2.4409	15.2565	-19.8593
19	0.097	0.2795	-0.5278	11.5981	1.1699	3.5447	-0.1701	0.1168	-0.4393	-1.0783	0.2725	-0.2045	0.4643	0.05	-0.1025	0.0755	-0.0565	-0.0539	0.0885	-0.0149	0.106	3.1921	7.9313	-28.0648
20	8.573	0.6917	-1.1454	8.7731	-3.0781	5.7001	-0.173	0.1387	-0.8363	-0.4557	0.0597	-0.2093	0.6521	-0.1839	0.1132	0.1496	-0.0408	-0.0557	-0.0246	-0.0303	0.2166	3.0979	-11.5837	-24.7809
21	11.6638	6.4785	-0.6083	5.1298	4.8996	17.9431	0.6126	-0.826	-0.4753	0.9618	-0.2586	-0.9269	0.2935	1.2658	-0.3539	0.0434	0.0445	-0.1583	0.3165	-0.0445	0.1217	4.6737	26.2584	15.7626
22	2.5525	2.5256	1.6844	7.3396	-0.2782	7.715	0.2973	-0.4066	0.206	0.1759	-0.0258	0.2592	-0.2975	-0.1691	-0.2715	0.1199	0.0376	-0.0261	0.1635	-0.0182	0.0185	-1.7026	31.1114	14.5366
23	4.6939	0.7026	0.0219	10.2463	5.9027	11.0083	0.5201	-0.1097	-0.1388	1.293	0.0716	0.6518	0.5004	-0.4541	-0.5917	0.2572	-0.05	-0.1418	0.1452	0.1499	0.0838	-3.2324	24.8113	11.3922
24	1.3475	-0.4296	-0.3015	10.2299	-1.7491	2.7789	-0.2554	0.0719	0.4209	-0.6308	0.3059	0.6175	-0.0984	0.1205	-0.0505	0.2566	0.0056	-0.1907	0.1808	0.0023	0.0643	-3.2611	32.2852	0.9861
25	4.4478	3.7799	2.9583	20.3416	6.5216	8.1278	-0.4241	-0.4178	0.2153	0.5715	0.417	-0.8653	-0.0624	1.0778	0.0071	0.2282	0.015	-0.0178	0.1552	-0.0844	0.3086	2.5724	50.9191	6.7115
26	10.4062	0.7475	2.7889	8.9861	3.2428	9.6971	0.5115	-0.2412	-0.0324	0.3777	-0.3787	0.9322	0.2261	-0.0006	-0.1329	0.3373	-0.0866	-0.0079	0.0394	-0.0913	0.3158	-5.4648	51.1548	7.8752
27	4.0095	-2.2344	0.1357	10.0233	8.9387	9.2615	-0.0614	0.2436	1.074	-0.4595	0.2434	0.4562	-0.8538	0.4471	-0.182	0.4177	-0.1939	-0.0966	0.0233	-0.0328	0.4157	-3.0765	58.6111	6.3279
28	26.1206	-9.2983	-1.4489	21.6449	10.155	5.148	0.8037	1.0994	1.0402	-1.2753	-0.8307	0.601	-1.4539	-0.4456	0.027	0.729	-0.0812	-0.2806	0.1595	0.123	0.2823	-8.9855	57.0446	-3.2941

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	238 - 257	21 - 40
2	X-RAY DIFFRACTION	2	A	A	258 - 283	41 - 66
3	X-RAY DIFFRACTION	3	A	A	284 - 345	67 - 128
4	X-RAY DIFFRACTION	4	A	A	346 - 370	129 - 153
5	X-RAY DIFFRACTION	5	A	A	371 - 404	154 - 187
6	X-RAY DIFFRACTION	6	A	A	405 - 424	188 - 207
7	X-RAY DIFFRACTION	7	A	A	433 - 474	216 - 257
8	X-RAY DIFFRACTION	8	B	B	237 - 256	20 - 39
9	X-RAY DIFFRACTION	9	B	B	257 - 292	40 - 75
10	X-RAY DIFFRACTION	10	B	B	293 - 346	76 - 129
11	X-RAY DIFFRACTION	11	B	B	347 - 368	130 - 151
12	X-RAY DIFFRACTION	12	B	B	369 - 384	152 - 167
13	X-RAY DIFFRACTION	13	B	B	385 - 401	168 - 184
14	X-RAY DIFFRACTION	14	B	B	402 - 424	185 - 207
15	X-RAY DIFFRACTION	15	B	B	433 - 474	216 - 257
16	X-RAY DIFFRACTION	16	C	C	236 - 257	19 - 40
17	X-RAY DIFFRACTION	17	C	C	258 - 284	41 - 67
18	X-RAY DIFFRACTION	18	C	C	285 - 350	68 - 133
19	X-RAY DIFFRACTION	19	C	C	351 - 382	134 - 165
20	X-RAY DIFFRACTION	20	C	C	383 - 474	166 - 257
21	X-RAY DIFFRACTION	21	D	D	238 - 258	21 - 41
22	X-RAY DIFFRACTION	22	D	D	259 - 303	42 - 86
23	X-RAY DIFFRACTION	23	D	D	304 - 344	87 - 127
24	X-RAY DIFFRACTION	24	D	D	345 - 383	128 - 166
25	X-RAY DIFFRACTION	25	D	D	384 - 399	167 - 182
26	X-RAY DIFFRACTION	26	D	D	400 - 424	183 - 207
27	X-RAY DIFFRACTION	27	D	D	433 - 458	216 - 241
28	X-RAY DIFFRACTION	28	D	D	459 - 474	242 - 257

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