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- PDB-6ami: Engineered tryptophan synthase b-subunit from Pyrococcus furiosus... -

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Basic information

Entry
Database: PDB / ID: 6ami
TitleEngineered tryptophan synthase b-subunit from Pyrococcus furiosus, PfTrpB4D11 with Trp non-covalently bound
ComponentsTryptophan synthase beta chain 1
KeywordsBIOSYNTHETIC PROTEIN / PLP Type II / Tryptophan Synthase / Engineered / Allostery
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / cytoplasm
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRYPTOPHAN / Tryptophan synthase beta chain 1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.97 Å
AuthorsBuller, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM110851 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble.
Authors: Buller, A.R. / van Roye, P. / Cahn, J.K.B. / Scheele, R.A. / Herger, M. / Arnold, F.H.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _pdbx_audit_support.grant_number / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,71113
Polymers174,7794
Non-polymers9329
Water3,945219
1
A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8446
Polymers87,3902
Non-polymers4544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-48 kcal/mol
Surface area25140 Å2
MethodPISA
2
C: Tryptophan synthase beta chain 1
hetero molecules

B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8677
Polymers87,3902
Non-polymers4775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_558x+1/2,-y+1/2,-z+31
Buried area1380 Å2
ΔGint-43 kcal/mol
Surface area27720 Å2
MethodPISA
3
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8677
Polymers87,3902
Non-polymers4775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-41 kcal/mol
Surface area24960 Å2
MethodPISA
4
C: Tryptophan synthase beta chain 1
D: Tryptophan synthase beta chain 1
hetero molecules

A: Tryptophan synthase beta chain 1
B: Tryptophan synthase beta chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,71113
Polymers174,7794
Non-polymers9329
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_558x+1/2,-y+1/2,-z+31
Buried area8740 Å2
ΔGint-100 kcal/mol
Surface area49090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.682, 109.921, 160.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Tryptophan synthase beta chain 1


Mass: 43694.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: trpB1, PF1706 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U093, tryptophan synthase
#2: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.85 / Details: 15-25% PEG3350 and 0.1 M Na HEPES pH 7.85

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→40 Å / Num. obs: 106192 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.047 / Net I/σ(I): 11.4
Reflection shellResolution: 1.97→2 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 5207 / CC1/2: 0.36 / Rpim(I) all: 1.338 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.97→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.844 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25089 5311 5 %RANDOM
Rwork0.21536 ---
obs0.21713 100105 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0 Å20 Å2
2--0.17 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.97→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11518 0 65 219 11802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01911841
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211216
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.96516060
X-RAY DIFFRACTIONr_angle_other_deg0.898325669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62551535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24223.908476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.684151830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8621557
X-RAY DIFFRACTIONr_chiral_restr0.0610.21779
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022676
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1690.8296167
X-RAY DIFFRACTIONr_mcbond_other0.1690.8286166
X-RAY DIFFRACTIONr_mcangle_it0.3121.2387690
X-RAY DIFFRACTIONr_mcangle_other0.3121.2387691
X-RAY DIFFRACTIONr_scbond_it0.1120.8515674
X-RAY DIFFRACTIONr_scbond_other0.1110.8515674
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2091.2798370
X-RAY DIFFRACTIONr_long_range_B_refined4.8927.05813202
X-RAY DIFFRACTIONr_long_range_B_other4.8836.94813153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 383 -
Rwork0.389 6890 -
obs--93.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.56520.76581.23372.83721.64643.2089-0.13760.36610.144-0.41970.111-0.1362-0.38550.46610.02660.4822-0.0830.08350.73560.13220.057693.74828.965183.798
20.95650.346-0.3263.70810.35751.64690.10110.257-0.0070.0345-0.0821-0.28280.08310.2774-0.0190.38030.04250.01930.64330.0270.236693.18211.424204.645
32.63591.6996-0.44041.8139-0.28893.50310.01890.05-0.0809-0.1633-0.1498-0.1101-0.46680.28150.13090.51540.02560.03160.5620.11740.172785.58430.611196.784
43.50640.74531.11396.65961.14.75620.03820.1682-0.1222-0.2176-0.06250.29730.1478-0.32860.02430.44410.0931-0.02720.55320.04140.216272.54225.177199.478
50.2705-0.47420.10652.7952-0.4161.7945-0.01520.26140.1089-0.4499-0.03590.0632-0.25170.10380.0510.49890.0156-0.01220.64980.10790.114684.28924.836190.466
62.80121.3113-0.87923.21890.10020.7305-0.04140.45770.0517-0.34140.0609-0.30710.1770.1767-0.01960.44740.13280.06650.732-0.0030.11395.1396.26192.242
79.23056.0126-2.09835.6615-4.18275.07560.12920.0523-0.0723-0.2196-0.1719-0.01680.40350.23370.04260.55850.0949-0.0430.6944-0.08280.101578.3159.102181.057
80.3054-0.84530.13072.85561.46258.54850.13850.06880.03-0.5031-0.16430.0762-0.1666-0.51680.02580.4702-0.0118-0.12680.76270.04740.241274.85911.045185.047
91.16660.0387-0.79011.0332-0.68363.7910.01650.3376-0.1634-0.2564-0.03490.08130.3913-0.02560.01830.45190.0514-0.01940.6093-0.06420.165985.064.082194.333
103.2309-0.7178-1.0353.18930.02062.25570.01660.3655-0.2376-0.1497-0.12450.14230.3077-0.04510.10790.44110.0167-0.03010.6071-0.05720.164685.7361.958201.883
111.0753-0.6309-1.09521.85431.4453.3688-0.1057-0.2023-0.09960.50030.0923-0.14280.48360.49740.01340.52090.0836-0.06040.53170.04860.207393.0376.052242.209
121.50020.0102-0.21881.8101-0.2192.20550.02340.19910.04830.0966-0.0366-0.1660.03880.35190.01310.40420.0074-0.0120.61140.0260.214392.78314.357220.416
132.9309-1.05-0.67252.17680.17464.38730.00290.0161-0.07350.1365-0.11620.24750.2608-0.38260.11330.4253-0.0650.00630.4725-0.03830.261475.7765.641224.651
141.14950.7846-0.51753.7197-0.93522.4999-0.1062-0.085-0.07660.22190.0324-0.09230.4630.25350.07380.48020.041-0.04010.51920.00510.260790.2087.647232.589
151.3062-1.33310.62021.66240.07882.5996-0.06530.05370.33940.08240.0451-0.453-0.47030.63360.02020.4503-0.1365-0.04980.58250.02110.294996.51127.887227.973
162.7009-3.30421.48265.1083-3.61045.22140.0088-0.1838-0.00220.20530.12790.2121-0.441-0.2188-0.13670.49530.00090.01080.4735-0.02080.218178.47423.207240.545
175.0756-1.08595.87161.8907-1.264320.65250.1404-1.06260.35540.16720.3229-0.06130.6803-0.4236-0.46330.6269-0.1140.04660.83310.02020.400671.89519.503243.613
181.7152-0.1450.5141.0302-0.29373.8496-0.0099-0.02110.28090.1339-0.0312-0.0061-0.3426-0.0150.04120.4716-0.0073-0.00170.41970.01660.296583.04227.887227.387
1910.43441.80773.60565.341-2.46133.33-0.25240.55730.35110.21940.0815-0.3896-0.34280.15680.17090.7031-0.08080.08380.360.05240.481891.21742.185223.241
204.8410.31781.06962.2978-0.08322.21010.13640.1710.3113-0.2064-0.13870.2262-0.1558-0.10410.00230.48370.0301-0.00480.51780.03560.301779.58726.023217.069
213.417-1.7771-1.21184.2894-0.60984.8195-0.3756-0.845-0.02910.54420.7890.2204-0.0101-0.7831-0.41340.38870.05760.05571.09580.07820.0883115.74743.198222.457
222.5251-1.61170.62322.2475-0.26992.21290.1204-0.0329-0.3087-0.19750.04030.28420.2975-0.4791-0.16070.4334-0.1429-0.02150.58290.0320.2507116.66932.557196.928
231.652-0.15080.15441.7489-0.25092.92830.0657-0.03960.23950.03620.0158-0.04730.0525-0.2896-0.08140.43750.00660.00050.50710.01220.2387122.36745.507202.801
242.2785-0.73040.7122.9207-0.47723.1-0.1959-0.32990.41260.31220.1384-0.2082-0.22810.19270.05760.41020.0335-0.03090.4383-0.04750.2728129.29451.702209.434
252.029-0.8713-0.10911.79551.44731.76820.0821-0.0831-0.35460.1967-0.05960.2810.5094-0.4462-0.02250.5973-0.1773-0.01850.56750.09230.2316118.45828.819206.148
267.27151.83841.3242.1246-0.17442.2921-0.0465-0.6483-0.2850.18420.07310.06030.3975-0.1995-0.02660.56780.04210.00660.4220.0410.2844130.29626.063213.311
2711.79-2.74641.76260.865-0.73263.8893-0.2244-0.60690.18520.18730.1546-0.3123-0.02990.11710.06980.52290.0153-0.05710.5276-0.02540.4027131.76337.455224.71
283.0469-0.2361-0.84862.2113-0.50145.14270.1121-0.59180.22270.12590.0837-0.12210.15530.1224-0.19580.50990.0411-0.04480.48750.01320.2207132.17134.459215.37
291.9459-0.4434-0.29071.6767-0.50732.7760.0554-0.024-0.3518-0.0679-0.0469-0.03370.55630.2064-0.00850.62220.0673-0.03830.3975-0.00390.2076134.94225.06202.797
303.50680.0851-0.66715.2160.19771.12540.12530.2234-0.264-0.0379-0.0983-0.23740.23810.1454-0.02690.58470.0345-0.06930.4911-0.01480.2112134.11527.422198.036
311.1333-0.2638-0.62041.8119-1.15733.26030.11360.3662-0.174-0.3656-0.08240.12540.90830.0124-0.03120.6766-0.0011-0.11080.5526-0.13330.0628125.56925.754166.422
321.5125-0.50030.09931.8077-0.67042.9822-0.00020.27380.15250.00110.07170.21940.232-0.3492-0.07160.4594-0.0022-0.03340.58860.02760.1948118.51743.857183.509
332.52461.0664-0.81841.62351.49556.0647-0.06830.3847-0.158-0.15780.0567-0.1030.06150.12890.01160.71450.1641-0.05070.5569-0.05480.0853134.38827.29174.222
343.32541.1519-1.21868.87740.9163.93260.03590.31670.0608-0.5424-0.0983-0.2079-0.32980.45950.06240.61520.1163-0.03360.5715-0.01560.0466141.27433.01180.773
351.9318-0.74210.78358.14174.19764.13020.46270.64440.1717-1.6823-0.3252-0.6053-0.56820.7316-0.13750.88230.20050.1630.88940.02590.0742143.5430.685168.441
360.8455-0.38420.65550.8280.31553.05870.12910.441-0.0217-0.2524-0.09440.16920.3449-0.2972-0.03470.4725-0.0049-0.05480.74750.04090.1211118.17740.505170.911
371.64083.05290.105811.00635.7786.10180.04710.20410.1417-0.07490.07220.0442-0.1290.1156-0.11930.42720.04070.00950.83960.16180.0966133.56849.813160.359
380.7497-0.21950.72452.08060.47464.12530.03280.3480.1659-0.39560.0051-0.2973-0.0790.4739-0.03790.4170.02960.03640.82340.12780.0798131.31947.222164.717
391.2706-0.21810.48861.17330.29024.06120.02810.29490.3419-0.0642-0.03840.1165-0.3647-0.20460.01030.36560.05970.00040.54330.14310.2948120.88353.5178.5
4014.08684.2573.07519.7917-0.32464.4489-0.06060.23030.93220.27680.1011-0.1737-0.29840.8877-0.04050.4424-0.0002-0.02170.57090.04550.3691136.40651.012187.096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 39
2X-RAY DIFFRACTION2A40 - 86
3X-RAY DIFFRACTION3A87 - 122
4X-RAY DIFFRACTION4A123 - 145
5X-RAY DIFFRACTION5A146 - 212
6X-RAY DIFFRACTION6A213 - 255
7X-RAY DIFFRACTION7A256 - 279
8X-RAY DIFFRACTION8A280 - 301
9X-RAY DIFFRACTION9A302 - 352
10X-RAY DIFFRACTION10A353 - 385
11X-RAY DIFFRACTION11B1 - 29
12X-RAY DIFFRACTION12B30 - 114
13X-RAY DIFFRACTION13B115 - 166
14X-RAY DIFFRACTION14B167 - 209
15X-RAY DIFFRACTION15B210 - 253
16X-RAY DIFFRACTION16B254 - 282
17X-RAY DIFFRACTION17B283 - 292
18X-RAY DIFFRACTION18B293 - 352
19X-RAY DIFFRACTION19B353 - 363
20X-RAY DIFFRACTION20B364 - 388
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