PDB-4ied: Crystal Structure of FUS-1 (OXA-85), a Class D beta-lactamase fro...

ID or keywords:

Entry

Database: PDB / ID: 4ied

Title

Crystal Structure of FUS-1 (OXA-85), a Class D beta-lactamase from Fusobacterium nucleatum subsp. polymorphum

Components

Class D beta-lactamase

Keywords

HYDROLASE / class D beta-lactamase / FUS-1 / OXA-85 /

antibiotic / beta-lactamase fold / Beta Lactamase Activity

Function / homology

Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain /

penicillin binding /

Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta / Class D beta-lactamase

Function and homology information

Biological species

Fusobacterium nucleatum subsp. polymorphum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Mangani, S. / Benvenuti, M. / Docquier, J.D.

Citation

Journal: To be Published
Title: Crystal Structure of FUS-1 (OXA-85), a Class D beta-lactamase from Fusobacterium nucleatum subsp. polymorphum
Authors: Mangani, S. / Benvenuti, M. / Docquier, J.D.

History

Deposition	Dec 13, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4ied.cif.gz	440.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4ied.ent.gz	376.9 KB	Display	PDB format
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Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ie/4ied ftp://data.pdbj.org/pub/pdb/validation_reports/ie/4ied	HTTPS FTP

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Related structure data

Similar structure data	5qaf-3 5qap-1 5qax-1 4s2j-4 6pt1-4 5qag-2 5qaq-3 6n6y-d 5qak-4 5qa8-4 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Class D beta-lactamase

B: Class D beta-lactamase

C: Class D beta-lactamase

D: Class D beta-lactamase

hetero molecules

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

1

A: Class D beta-lactamase

hetero molecules

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

2

B: Class D beta-lactamase

hetero molecules

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

3

C: Class D beta-lactamase

hetero molecules

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

4

D: Class D beta-lactamase

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.945, 65.670, 91.698
Angle α, β, γ (deg.)	84.59, 82.91, 70.12
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Class D beta-lactamase Mass: 29770.119 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusobacterium nucleatum subsp. polymorphum (bacteria) Gene: fus1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6XL56, beta-lactamase

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Non-polymers , 5 types, 1706 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1689 / 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: 2.07 Å³/Da / Density % sol: 40.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: FUS-1 15mg/mL in 10 mM Tris pH=8.0, 0.1M NaCl, 4.0 M Na/NH4 formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2005
Radiation	Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 1.5→37.59 Å / Num. all: 146121 / Num. obs: 146121 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / B_iso Wilson estimate: 11.448 Å² / R_merge(I) obs: 0.062 / Net I/σ(I): 17.7
Reflection shell	Resolution: 1.5→1.58 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.246 / Mean I/σ(I) obs: 6.1 / Num. unique all: 21066 / % possible all: 94

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Processing

Software

Name	Version	Classification
PXSOFT		data collection
MOLREP		phasing
REFMAC	5.7.0029	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→37.59 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.947 / SU B: 2.165 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18428	13309	9.1 %	RANDOM
R_work	0.14615	-	-	-
obs	0.14961	132805	95.48 %	-

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: 12.78 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	-0.02 Å²	0.03 Å²
2-	-	0 Å²	-0.01 Å²
3-	-	-	-0.02 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.08 Å	0.076 Å

Refinement step

Cycle: LAST / Resolution: 1.5→37.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8081	0	26	1689	9796

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.02	8535
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8326
X-RAY DIFFRACTION	r_angle_refined_deg	2.131	1.967	11527
X-RAY DIFFRACTION	r_angle_other_deg	0.982	3	19269
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.969	5	1048
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.407	25.256	430
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.238	15	1668
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.08	15	35
X-RAY DIFFRACTION	r_chiral_restr	0.151	0.2	1220
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	9617
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1986

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.216	953	-
R_work	0.17	9649	-
obs	-	-	93.76 %

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	2.8214	-3.4575	1.2101	5.7699	-0.6352	7.0965	-0.1432	-0.2527	0.1352	0.4428	0.0624	0.1994	-0.1397	-0.3171	0.0808	0.0757	-0.0122	0.0608	0.1198	-0.0464	0.1159	-11.852	3.565	18.129
2	3.5994	-4.9032	1.81	11.8539	9.7242	29.6306	-0.3185	-0.138	0.0661	-0.1186	0.1785	-0.0313	-1.4766	-0.104	0.14	0.1216	0.0666	0.0275	0.2112	-0.0864	0.2965	-15.681	9.736	12.318
3	0.6626	0.044	-0.1302	0.5348	0.1137	0.7214	-0.0216	-0.0347	-0.0481	0.0693	0.0009	0.0199	0.0827	-0.0551	0.0207	0.0245	0.0031	-0.0115	0.0273	0.0075	0.0662	-2.452	-4.41	3.761
4	0.0705	0.0409	-0.2023	1.4479	0.1844	0.8091	-0.0009	0.0178	0.0076	-0.1328	-0.026	0.0363	0.0106	-0.009	0.0269	0.0234	0.0146	-0.0088	0.035	-0.0013	0.0669	6.584	7.207	-14.223
5	1.3774	0.9714	-1.5528	2.096	-2.0974	3.837	-0.0044	0.0226	-0.0718	-0.097	-0.0137	-0.1294	0.0974	0.0444	0.0181	0.0128	0.0048	-0.0147	0.0193	-0.0076	0.0723	2.459	-12.262	-11.855
6	0.9031	0.0518	0.04	0.644	-0.0149	0.8557	-0.0066	-0.0011	-0.023	-0.012	0.0158	-0.0051	0.0975	0.0014	-0.0092	0.0173	0.0069	-0.0139	0.0195	0.0018	0.0568	-0.753	-7.586	-3.76
7	2.2709	0.489	-0.4111	7.4569	-4.1317	6.9799	0.088	-0.0875	-0.1094	0.0764	-0.1967	-0.3464	0.3403	0.7322	0.1086	0.0381	0.0482	-0.0257	0.0911	-0.0089	0.0844	15.137	-5.057	-1.915
8	0.5316	0.0253	0.0003	0.6667	0.0313	0.7172	-0.0206	-0.0241	0.044	0.0684	0.0002	0.0435	-0.0402	-0.0149	0.0204	0.0149	0.0073	-0.011	0.0348	0.0025	0.0596	-1.171	5.808	5.664
9	10.82	-3.1022	4.4829	5.8917	-3.2578	15.7897	-0.2383	0.0119	0.535	0.2514	-0.1322	-0.2372	-0.5527	0.2451	0.3705	0.0439	0.0007	-0.034	0.0376	-0.0037	0.0571	2.699	8.155	19.601
10	8.5543	6.7436	0.1955	8.8382	0.5144	4.0747	0.1036	0.3779	0.1068	-0.4165	-0.1476	0.1071	-0.1839	-0.043	0.044	0.1098	0.071	-0.0284	0.1032	0.0269	0.0463	6.967	37.081	-33.684
11	8.8412	-1.0514	-5.155	0.9715	2.5276	16.7903	-0.0201	0.5969	-0.2732	-0.102	-0.1918	0.3632	0.4363	-0.7703	0.2119	0.0614	0.016	-0.0849	0.1608	-0.0243	0.1979	-4.349	31.185	-29.315
12	0.35	-0.0343	-0.047	0.8178	0.0202	0.5532	0.0044	0.0311	0.0505	-0.091	-0.0258	-0.0417	-0.0495	-0.0076	0.0214	0.0167	0.0034	-0.0096	0.03	0.0093	0.067	12.621	33.297	-17.18
13	0.5881	0.2046	0.1388	0.7788	-0.339	0.4202	0.0065	-0.0428	0.0226	0.0835	-0.0272	-0.0054	-0.0491	0.0231	0.0207	0.0142	0.0035	-0.0152	0.0308	-0.0022	0.0616	10.197	20.2	0.981
14	0.1543	0.4617	-0.5276	2.9375	-2.0887	4.6486	0.0207	-0.0286	0.0208	0.0934	-0.0563	-0.0973	0.0054	0.177	0.0356	0.0175	-0.0037	-0.0235	0.043	0.0021	0.0745	20.311	38.183	-2.68
15	0.8967	-0.2572	-0.0634	1.476	0.1851	1.0694	-0.007	0.0341	0.0043	0.0174	-0.0161	-0.0276	-0.0722	0.0406	0.0231	0.0097	-0.0058	-0.0188	0.0309	0.0014	0.0704	13.546	36.036	-9.965
16	3.2198	-4.9038	-3.9338	22.3782	7.3804	4.9379	-0.0846	-0.3146	-0.0659	0.2324	0.0753	-0.4904	0.1098	0.3435	0.0093	0.0048	0.0136	0.0065	0.1233	0.0109	0.1373	28.601	27.089	-10.21
17	1.0685	0.4153	0.7285	1.3233	0.746	1.2006	0.0313	0.0664	-0.0333	-0.0897	-0.0173	-0.1695	0.0829	0.1443	-0.014	0.033	0.0255	0.0161	0.0589	0.0076	0.0883	18.526	18.469	-17.434
18	0.9197	-0.1331	-0.4915	0.985	0.2835	1.049	-0.006	0.026	0.0233	-0.0801	-0.0388	0.0585	0.0001	-0.0214	0.0448	0.0124	0.009	-0.0187	0.0341	0.0051	0.0671	7.197	27.872	-18.369
19	2.6725	-0.071	-2.4368	1.3916	0.3423	3.4909	-0.0093	0.1672	-0.0359	-0.2111	-0.0512	0.1362	0.0418	-0.1559	0.0605	0.0453	0.0158	-0.0399	0.0459	-0.0063	0.0769	3.139	22.857	-26.084
20	5.7337	-3.4885	1.6719	3.9152	-0.9737	2.0937	-0.0531	-0.1042	-0.2153	0.2634	0.0663	0.1618	-0.1539	-0.1984	-0.0132	0.0448	0.0082	0.0013	0.0774	0.0246	0.0485	-20.794	-8.117	-26.952
21	0.3354	0.0698	-0.1595	0.5281	-0.3517	1.0328	-0.0111	-0.04	-0.0308	-0.0296	0.0198	0.0061	0.0606	-0.0189	-0.0088	0.028	0.012	-0.0289	0.0478	0.0089	0.0483	-11.925	-5.939	-40.85
22	1.1628	-0.6295	0.4347	1.1316	-0.5203	0.9081	0.0346	0.0253	-0.0031	-0.0728	-0.0431	0.0026	-0.0053	0.0432	0.0085	0.0593	0.0152	-0.0182	0.0382	-0.004	0.0433	-10.467	10.783	-58.13
23	0.5065	-0.4694	0.0594	0.664	-0.5786	1.2338	0.0352	0.0518	-0.0106	-0.0391	-0.0473	-0.0026	0.0611	0.0294	0.0121	0.0647	0.0294	-0.0203	0.0403	-0.0041	0.0475	-6.244	-7.225	-57.485
24	1.3579	0.4569	0.2341	0.8376	0.2007	1.0116	0.0162	-0.0737	-0.0299	0.0121	-0.0287	-0.0455	0.0986	0.0924	0.0125	0.037	0.0267	-0.0293	0.0547	0.0112	0.0625	-4.964	-5.845	-44.05
25	2.4892	-1.1936	-0.8274	1.0851	0.1414	0.7109	-0.0163	-0.0307	0.0928	0.0911	-0.0344	-0.0901	-0.0674	0.0591	0.0507	0.052	0.0063	-0.0376	0.0606	0.0021	0.06	-3.309	7.776	-42.493
26	1.0453	-0.0026	0.4377	0.8114	0.0329	1.2443	-0.0135	-0.0786	-0.038	0.0127	0.0625	0.0383	-0.0968	-0.1007	-0.049	0.0314	0.0117	-0.0221	0.0585	0.0104	0.0348	-16.625	1.1	-40.271
27	1.0448	0.0692	0.5192	1.2278	-0.5206	3.3913	-0.0371	-0.0877	-0.0801	0.0968	0.118	0.102	-0.2012	-0.3108	-0.0809	0.0292	0.0365	-0.0055	0.0941	0.0186	0.049	-20.302	3.53	-33.921
28	15.6261	3.6842	-0.8671	6.7728	-2.8505	15.1926	-0.0023	-0.5253	0.3906	0.2897	-0.0109	-0.0132	-0.7065	-0.0308	0.0132	0.0551	0.0294	-0.0159	0.0734	-0.0212	0.0231	-15.246	6.561	-25.048
29	1.5331	0.27	0.9356	0.5252	0.5984	1.2398	-0.0035	0.0584	0.0217	-0.2191	-0.0444	0.0611	-0.1288	-0.0644	0.0479	0.1271	0.0096	-0.0438	0.0351	0.0152	0.0404	-27.174	27.71	-74.985
30	0.5708	-0.088	0.2752	0.5793	0.393	1.0671	-0.0468	0.0025	0.0227	-0.0537	0.0198	0.0304	-0.132	0.0059	0.027	0.0767	0.007	-0.0258	0.0156	0.0082	0.0373	-23.072	32.859	-58.563
31	3.179	3.1153	-2.4146	4.8634	-2.9757	3.4818	-0.0366	-0.1779	-0.0208	0.2306	-0.0479	-0.1339	-0.129	0.1684	0.0845	0.0518	0.0302	-0.0337	0.0594	-0.0187	0.0403	-10.04	21.989	-41.237
32	0.3978	-0.3002	-0.0492	1.5975	-0.1105	0.7571	-0.0144	-0.0186	-0.0195	0.0639	0.0624	0.0632	-0.0296	0.0094	-0.048	0.0576	0.0292	-0.0132	0.0451	-0.0016	0.0421	-17.484	19.768	-45.442
33	0.7777	-0.4069	0.3466	0.9736	-0.5908	1.5811	-0.0062	-0.0364	0.0352	0.058	-0.0116	-0.0291	-0.1024	0.0548	0.0178	0.0847	0.0148	-0.0176	0.0258	-0.0074	0.0456	-20.765	40.273	-47.689
34	0.8876	-0.1943	-0.6963	0.6277	0.0886	1.5625	0.0156	-0.0223	0.0127	-0.0146	-0.0015	0.0041	-0.1354	0.026	-0.0141	0.0768	0.005	-0.0191	0.011	-0.0006	0.0411	-22.459	34.993	-54.925
35	13.6213	-15.3993	-5.8879	17.4843	6.1444	6.7856	-0.2423	-0.5296	0.6644	0.2729	0.5456	-0.7635	-0.1301	0.6676	-0.3033	0.1219	-0.0583	-0.037	0.1233	-0.016	0.1283	-5.454	38.417	-53.153
36	0.336	0.0773	-0.1056	0.7702	0.0577	0.9475	-0.0185	0.0305	0.0357	-0.0969	0.0091	-0.0105	-0.0214	0.048	0.0094	0.0671	0.0066	-0.0156	0.0307	0.0052	0.0319	-17.951	25.494	-62.744
37	1.4392	-0.1157	-1.8394	1.4951	0.0079	5.0684	-0.0067	0.0642	-0.0432	-0.1142	-0.0157	0.0539	0.1089	-0.0671	0.0224	0.0624	0.0062	-0.0424	0.0261	0.0025	0.035	-22.397	18.982	-70.734

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	13 - 22
2	X-RAY DIFFRACTION	2	A	23 - 28
3	X-RAY DIFFRACTION	3	A	29 - 73
4	X-RAY DIFFRACTION	4	A	74 - 116
5	X-RAY DIFFRACTION	5	A	117 - 131
6	X-RAY DIFFRACTION	6	A	132 - 173
7	X-RAY DIFFRACTION	7	A	174 - 178
8	X-RAY DIFFRACTION	8	A	179 - 247
9	X-RAY DIFFRACTION	9	A	248 - 254
10	X-RAY DIFFRACTION	10	B	10 - 18
11	X-RAY DIFFRACTION	11	B	19 - 28
12	X-RAY DIFFRACTION	12	B	29 - 74
13	X-RAY DIFFRACTION	13	B	75 - 118
14	X-RAY DIFFRACTION	14	B	119 - 131
15	X-RAY DIFFRACTION	15	B	132 - 170
16	X-RAY DIFFRACTION	16	B	171 - 174
17	X-RAY DIFFRACTION	17	B	175 - 190
18	X-RAY DIFFRACTION	18	B	191 - 232
19	X-RAY DIFFRACTION	19	B	233 - 254
20	X-RAY DIFFRACTION	20	C	8 - 24
21	X-RAY DIFFRACTION	21	C	25 - 73
22	X-RAY DIFFRACTION	22	C	74 - 110
23	X-RAY DIFFRACTION	23	C	111 - 145
24	X-RAY DIFFRACTION	24	C	146 - 174
25	X-RAY DIFFRACTION	25	C	175 - 187
26	X-RAY DIFFRACTION	26	C	188 - 237
27	X-RAY DIFFRACTION	27	C	238 - 247
28	X-RAY DIFFRACTION	28	C	248 - 254
29	X-RAY DIFFRACTION	29	D	13 - 39
30	X-RAY DIFFRACTION	30	D	40 - 73
31	X-RAY DIFFRACTION	31	D	74 - 85
32	X-RAY DIFFRACTION	32	D	86 - 116
33	X-RAY DIFFRACTION	33	D	117 - 136
34	X-RAY DIFFRACTION	34	D	137 - 170
35	X-RAY DIFFRACTION	35	D	171 - 174
36	X-RAY DIFFRACTION	36	D	175 - 232
37	X-RAY DIFFRACTION	37	D	233 - 254

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