PDB-8bbl: SGL a GH20 family sulfoglycosidase

ID or keywords:

Entry

Database: PDB / ID: 8bbl

Title

SGL a GH20 family sulfoglycosidase

Components

Beta-N-acetylhexosaminidase

Hexosaminidase

Keywords

HYDROLASE / GH20

Function / homology

Function and homology information

beta-N-acetylhexosaminidase activity /

N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process
Similarity search - Function

Biological species

Prevotella (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.711 Å

Authors

Dong, M.D. / Roth, C.R. / Jin, Y.J.

Funding support

United Kingdom, 3items

Citation

Journal: Acs Catalysis / Year: 2022
Title: Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases
Authors: Zhang, Z. / Dong, M. / Zallot, R. / Blackburn, G.M. / Wang, N. / Wang, C. / Chen, L. / Baumann, P. / Wu, Z. / Wang, Z. / Fan, H. / Roth, C. / Jin, Y. / He, Y.

History

Deposition	Oct 13, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 11, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8bbl.cif.gz	854 KB	Display	PDBx/mmCIF format
PDB format	pdb8bbl.ent.gz	639.7 KB	Display	PDB format
PDBx/mmJSON format	8bbl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bb/8bbl ftp://data.pdbj.org/pub/pdb/validation_reports/bb/8bbl	HTTPS FTP

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Related structure data

Related structure data	7dupC 7dvaC 7dvbC 8balC 8bdpC C: citing same article (ref.)
Similar structure data	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	#141 - Sep 2011 O-GlcNAc Transferase similarity (3)

Deposited unit

A: Beta-N-acetylhexosaminidase

B: Beta-N-acetylhexosaminidase

C: Beta-N-acetylhexosaminidase

D: Beta-N-acetylhexosaminidase

E: Beta-N-acetylhexosaminidase

F: Beta-N-acetylhexosaminidase

H: Beta-N-acetylhexosaminidase

G: Beta-N-acetylhexosaminidase

796 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-N-acetylhexosaminidase

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

2

B: Beta-N-acetylhexosaminidase

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

3

C: Beta-N-acetylhexosaminidase

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

4

D: Beta-N-acetylhexosaminidase

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

5

E: Beta-N-acetylhexosaminidase

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

6

F: Beta-N-acetylhexosaminidase

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

7

H: Beta-N-acetylhexosaminidase

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

8

G: Beta-N-acetylhexosaminidase

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

Unit cell

Length a, b, c (Å)	132.950, 133.420, 225.370
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	129 - 676
2	1	1	1	A	129 - 676
3	2	2	1	A	129 - 676
4	2	2	1	A	129 - 676
5	3	3	1	A	129 - 676
6	3	3	1	A	129 - 676
7	4	4	1	A	129 - 676
8	4	4	1	A	129 - 676
9	5	5	1	A	129 - 676
10	5	5	1	A	129 - 676
11	6	6	1	A	129 - 676
12	6	6	1	A	129 - 676
13	7	7	1	A	129 - 676
14	7	7	1	A	129 - 676
15	8	8	1	A	129 - 675
16	8	8	1	A	129 - 675
17	9	9	1	A	129 - 675
18	9	9	1	A	129 - 675
19	10	10	1	A	129 - 675
20	10	10	1	A	129 - 675
21	11	11	1	A	129 - 675
22	11	11	1	A	129 - 675
23	12	12	1	A	129 - 677
24	12	12	1	A	129 - 677
25	13	13	1	A	129 - 675
26	13	13	1	A	129 - 675
27	14	14	1	A	129 - 676
28	14	14	1	A	129 - 676
29	15	15	1	A	129 - 676
30	15	15	1	A	129 - 676
31	16	16	1	A	129 - 676
32	16	16	1	A	129 - 676
33	17	17	1	A	129 - 675
34	17	17	1	A	129 - 675
35	18	18	1	A	129 - 676
36	18	18	1	A	129 - 676
37	19	19	1	A	129 - 676
38	19	19	1	A	129 - 676
39	20	20	1	A	129 - 676
40	20	20	1	A	129 - 676
41	21	21	1	A	129 - 675
42	21	21	1	A	129 - 675
43	22	22	1	A	129 - 676
44	22	22	1	A	129 - 676
45	23	23	1	A	129 - 676
46	23	23	1	A	129 - 676
47	24	24	1	A	129 - 675
48	24	24	1	A	129 - 675
49	25	25	1	A	129 - 676
50	25	25	1	A	129 - 676
51	26	26	1	A	129 - 675
52	26	26	1	A	129 - 675
53	27	27	1	A	129 - 676
54	27	27	1	A	129 - 676
55	28	28	1	A	129 - 675
56	28	28	1	A	129 - 675

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56

#1: Protein	Beta-N-acetylhexosaminidase / Hexosaminidase Mass: 99524.680 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Prevotella (bacteria) / Gene: sgl / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5MAH5, beta-N-acetylhexosaminidase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 18 / 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: 5.02 Å³/Da
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 23.7 mg/mL protein in the buffer of Tris-HCl 25 mM, pH 8.0, and NaCl 200 mM was mixed 1:1 with the precipitant containing 0.1 M Bis-tris, pH 6.5, and 18-21.5% w/v PEG5000 MME.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I03 / Wavelength: 0.9762 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 17, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.1821
pseudo-merohedral	2	2	h,-k,-l	2	0.177
pseudo-merohedral	3	3	-H, K, -L	3	0.1787
pseudo-merohedral	4	4	-h,-k,l	4	0.1773
pseudo-merohedral	5	5	K, H, -L	5	0.0712
pseudo-merohedral	6	6	k,-h,l	6	0.0715
pseudo-merohedral	7	7	-K, H, L	7	0.0703
pseudo-merohedral	8	8	-K, -H, -L	8	0.072

Reflection

Resolution: 2.71→94.18 Å / Num. obs: 406028 / % possible obs: 97.6 % / Redundancy: 1.9 % / CC_1/2: 0.981 / Net I/σ(I): 5.1

Reflection shell

Resolution: 2.71→2.77 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 20183 / CC_1/2: 0.343 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
xia2		data reduction
xia2		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 2.711→94.176 Å / Cor.coef. F_o:F_c: 0.729 / Cor.coef. F_o:F_c free: 0.658 / WR_factor R_free: 0.303 / WR_factor R_work: 0.267 / SU B: 4.045 / SU ML: 0.096 / Average fsc free: 0.9392 / Average fsc work: 0.952 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3187	20528	5.056 %
R_work	0.283	385494	-
all	0.285	-	-
obs	-	406022	96.588 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 25.682 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.498 Å²	1.226 Å²	-6.7 Å²
2-	-	-16.627 Å²	-0.939 Å²
3-	-	-	16.129 Å²

Refinement step

Cycle: LAST / Resolution: 2.711→94.176 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	31754	0	0	18	31772

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	32583
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	28590
X-RAY DIFFRACTION	r_angle_refined_deg	1.761	1.651	44239
X-RAY DIFFRACTION	r_angle_other_deg	0.587	1.563	66624
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	13.098	5	3970
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.523	5	160
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.604	10	5128
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.494	10	1589
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	4632
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	37349
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	6772
X-RAY DIFFRACTION	r_nbd_refined	0.338	0.2	12390
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.254	0.2	35127
X-RAY DIFFRACTION	r_nbtor_refined	0.204	0.2	16061
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.092	0.2	17777
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.309	0.2	1666
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.152	0.2	102
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.339	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.37	0.2	28
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.351	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.863	2.693	16021
X-RAY DIFFRACTION	r_mcbond_other	1.863	2.693	16021
X-RAY DIFFRACTION	r_mcangle_it	2.928	4.036	19944
X-RAY DIFFRACTION	r_mcangle_other	2.928	4.036	19945
X-RAY DIFFRACTION	r_scbond_it	1.401	2.643	16562
X-RAY DIFFRACTION	r_scbond_other	1.401	2.643	16563
X-RAY DIFFRACTION	r_scangle_it	2.156	3.976	24295
X-RAY DIFFRACTION	r_scangle_other	2.156	3.976	24296
X-RAY DIFFRACTION	r_lrange_it	4.545	33.174	43284
X-RAY DIFFRACTION	r_lrange_other	4.545	33.174	43285
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.246	0.05	12305
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.244	0.05	12322
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.247	0.05	12332
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.248	0.05	12281
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.248	0.05	12332
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.248	0.05	12217
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.244	0.05	12357
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.164	0.05	14288
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.167	0.05	14168
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.165	0.05	14159
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.163	0.05	14246
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.171	0.05	14177
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.156	0.05	14408
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.163	0.05	14361
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.163	0.05	14301
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.158	0.05	14409
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.161	0.05	14291
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.15	0.05	14584
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.166	0.05	14276
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.163	0.05	14337
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.167	0.05	14218
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.154	0.05	14420
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.166	0.05	14284
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.173	0.05	14095
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.16	0.05	14433
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.165	0.05	14256
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.153	0.05	14569
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.158	0.05	14339

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.24633	0.05005
1	2	A	X-RAY DIFFRACTION	Local ncs	0.24633	0.05005
2	3	A	X-RAY DIFFRACTION	Local ncs	0.24427	0.05005
2	4	A	X-RAY DIFFRACTION	Local ncs	0.24427	0.05005
3	5	A	X-RAY DIFFRACTION	Local ncs	0.24688	0.05005
3	6	A	X-RAY DIFFRACTION	Local ncs	0.24688	0.05005
4	7	A	X-RAY DIFFRACTION	Local ncs	0.2478	0.05005
4	8	A	X-RAY DIFFRACTION	Local ncs	0.2478	0.05005
5	9	A	X-RAY DIFFRACTION	Local ncs	0.24757	0.05005
5	10	A	X-RAY DIFFRACTION	Local ncs	0.24757	0.05005
6	11	A	X-RAY DIFFRACTION	Local ncs	0.24849	0.05005
6	12	A	X-RAY DIFFRACTION	Local ncs	0.24849	0.05005
7	13	A	X-RAY DIFFRACTION	Local ncs	0.2438	0.05005
7	14	A	X-RAY DIFFRACTION	Local ncs	0.2438	0.05005
8	15	A	X-RAY DIFFRACTION	Local ncs	0.16362	0.05006
8	16	A	X-RAY DIFFRACTION	Local ncs	0.16362	0.05006
9	17	A	X-RAY DIFFRACTION	Local ncs	0.16704	0.05006
9	18	A	X-RAY DIFFRACTION	Local ncs	0.16704	0.05006
10	19	A	X-RAY DIFFRACTION	Local ncs	0.16499	0.05006
10	20	A	X-RAY DIFFRACTION	Local ncs	0.16499	0.05006
11	21	A	X-RAY DIFFRACTION	Local ncs	0.16271	0.05006
11	22	A	X-RAY DIFFRACTION	Local ncs	0.16271	0.05006
12	23	A	X-RAY DIFFRACTION	Local ncs	0.17113	0.05006
12	24	A	X-RAY DIFFRACTION	Local ncs	0.17113	0.05006
13	25	A	X-RAY DIFFRACTION	Local ncs	0.15641	0.05006
13	26	A	X-RAY DIFFRACTION	Local ncs	0.15641	0.05006
14	27	A	X-RAY DIFFRACTION	Local ncs	0.16323	0.05006
14	28	A	X-RAY DIFFRACTION	Local ncs	0.16323	0.05006
15	29	A	X-RAY DIFFRACTION	Local ncs	0.16336	0.05006
15	30	A	X-RAY DIFFRACTION	Local ncs	0.16336	0.05006
16	31	A	X-RAY DIFFRACTION	Local ncs	0.15829	0.05006
16	32	A	X-RAY DIFFRACTION	Local ncs	0.15829	0.05006
17	33	A	X-RAY DIFFRACTION	Local ncs	0.16148	0.05006
17	34	A	X-RAY DIFFRACTION	Local ncs	0.16148	0.05006
18	35	A	X-RAY DIFFRACTION	Local ncs	0.1496	0.05006
18	36	A	X-RAY DIFFRACTION	Local ncs	0.1496	0.05006
19	37	A	X-RAY DIFFRACTION	Local ncs	0.16624	0.05006
19	38	A	X-RAY DIFFRACTION	Local ncs	0.16624	0.05006
20	39	A	X-RAY DIFFRACTION	Local ncs	0.16272	0.05006
20	40	A	X-RAY DIFFRACTION	Local ncs	0.16272	0.05006
21	41	A	X-RAY DIFFRACTION	Local ncs	0.16705	0.05006
21	42	A	X-RAY DIFFRACTION	Local ncs	0.16705	0.05006
22	43	A	X-RAY DIFFRACTION	Local ncs	0.1544	0.05006
22	44	A	X-RAY DIFFRACTION	Local ncs	0.1544	0.05006
23	45	A	X-RAY DIFFRACTION	Local ncs	0.16552	0.05006
23	46	A	X-RAY DIFFRACTION	Local ncs	0.16552	0.05006
24	47	A	X-RAY DIFFRACTION	Local ncs	0.17269	0.05006
24	48	A	X-RAY DIFFRACTION	Local ncs	0.17269	0.05006
25	49	A	X-RAY DIFFRACTION	Local ncs	0.16037	0.05006
25	50	A	X-RAY DIFFRACTION	Local ncs	0.16037	0.05006
26	51	A	X-RAY DIFFRACTION	Local ncs	0.16481	0.05006
26	52	A	X-RAY DIFFRACTION	Local ncs	0.16481	0.05006
27	53	A	X-RAY DIFFRACTION	Local ncs	0.15261	0.05006
27	54	A	X-RAY DIFFRACTION	Local ncs	0.15261	0.05006
28	55	A	X-RAY DIFFRACTION	Local ncs	0.15773	0.05006
28	56	A	X-RAY DIFFRACTION	Local ncs	0.15773	0.05006

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.711-2.781	0.516	1291	0.446	25001	X-RAY DIFFRACTION	84.3558
2.781-2.857	0.419	1431	0.348	28243	X-RAY DIFFRACTION	97.892
2.857-2.94	0.364	1421	0.299	27246	X-RAY DIFFRACTION	97.071
2.94-3.031	0.334	1480	0.286	26573	X-RAY DIFFRACTION	98.1526
3.031-3.13	0.324	1477	0.269	25523	X-RAY DIFFRACTION	97.5962
3.13-3.24	0.309	1499	0.259	24849	X-RAY DIFFRACTION	97.8934
3.24-3.362	0.295	1325	0.263	24101	X-RAY DIFFRACTION	98.1169
3.362-3.499	0.276	1273	0.255	22916	X-RAY DIFFRACTION	97.0355
3.499-3.655	0.267	1137	0.253	21987	X-RAY DIFFRACTION	97.2823
3.655-3.833	0.275	1077	0.258	21208	X-RAY DIFFRACTION	97.4378
3.833-4.04	0.27	994	0.254	20249	X-RAY DIFFRACTION	97.4897
4.04-4.285	0.267	911	0.267	18674	X-RAY DIFFRACTION	95.156
4.285-4.581	0.313	1058	0.267	17844	X-RAY DIFFRACTION	97.9023
4.581-4.948	0.27	914	0.266	16758	X-RAY DIFFRACTION	98.2542
4.948-5.42	0.309	743	0.272	15246	X-RAY DIFFRACTION	97.1149
5.42-6.06	0.34	756	0.283	13840	X-RAY DIFFRACTION	97.5082
6.06-6.996	0.371	645	0.29	12337	X-RAY DIFFRACTION	98.3783
6.996-8.566	0.344	486	0.301	10492	X-RAY DIFFRACTION	98.8297
8.566-12.106	0.371	382	0.314	8037	X-RAY DIFFRACTION	97.9295
12.106-94.176	0.467	228	0.429	4370	X-RAY DIFFRACTION	97.6843

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