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- PDB-3zk8: CRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA E205Q IN T... -

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Basic information

Entry
Database: PDB / ID: 3zk8
TitleCRYSTAL STRUCTURE OF PNEUMOCOCCAL SURFACE ANTIGEN PSAA E205Q IN THE METAL-FREE, OPEN STATE
ComponentsMANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
KeywordsMETAL TRANSPORT / ATP-BINDING CASSETTE TRANSPORTERS / BACTERIAL ADHESION / CARRIER PROTEINS / LIPOPROTEINS / MEMBRANE TRANSPORT PROTEINS
Function / homology
Function and homology information


metal ion transport / cell adhesion / metal ion binding / plasma membrane
Similarity search - Function
Adhesin B / Adhesion lipoprotein / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Manganese ABC transporter substrate-binding lipoprotein PsaA
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsCounago, R.M. / Ween, M.P. / Bajaj, M. / Zuegg, J. / Cooper, M.A. / McEwan, A.G. / Paton, J.C. / Kobe, B. / McDevitt, C.A.
Citation
Journal: Nat. Chem. Biol. / Year: 2014
Title: Imperfect coordination chemistry facilitates metal ion release in the Psa permease.
Authors: Counago, R.M. / Ween, M.P. / Begg, S.L. / Bajaj, M. / Zuegg, J. / O'Mara, M.L. / Cooper, M.A. / McEwan, A.G. / Paton, J.C. / Kobe, B. / McDevitt, C.A.
#1: Journal: Structure / Year: 1998
Title: The Crystal Structure of Pneumococcal Surface Antigen Psaa Reveals a Metal-Binding Site and a Novel Structure for a Putative Abc-Type Binding Protein.
Authors: Lawrence, M.C. / Pilling, P.A. / Epa, V.C. / Berry, A.M. / Ogunniyi, A.D. / Paton, J.C.
#2: Journal: Plos Pathog. / Year: 2011
Title: A Molecular Mechanism for Bacterial Susceptibility to Zinc.
Authors: McDevitt, C.A. / Ogunniyi, A.D. / Valkov, E. / Lawrence, M.C. / Kobe, B. / McEwan, A.G. / Paton, J.C.
History
DepositionJan 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Jan 8, 2014Group: Database references
Revision 2.0Mar 28, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / citation / citation_author
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _audit_author.name / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.1Mar 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
B: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1334
Polymers62,8892
Non-polymers2442
Water12,394688
1
A: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5672
Polymers31,4441
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5672
Polymers31,4441
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.770, 59.070, 62.210
Angle α, β, γ (deg.)106.40, 105.05, 93.55
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.007, -0.004), (0.007, -1, -0.022), (-0.004, 0.022, -1)
Vector: 0.655, -23.496, 47.857)

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Components

#1: Protein MANGANESE ABC TRANSPORTER SUBSTRATE-BINDING LIPOPROTEIN / PSAA / PNEUMOCOCCAL SURFACE ADHESIN A


Mass: 31444.402 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-309 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A4G2
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 42.25 % / Description: NONE
Crystal growTemperature: 293 K
Details: 12.5% W/V PEG 1,000 12.5% W/V PEG 3,350, 12.5% V/V MPD; 0.1 M TRIZMA/BICINE PH 8.7 AFTER 7-10 DAYS AT 293 K, FOLLOWING STREAK-SEEDING OF PRE-EQUILIBRATED (24 HOURS) DROPS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: SILICON MIRRORS (ADAPTIVE AND U-BENT)
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR (SI111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→19.65 Å / Num. obs: 57680 / % possible obs: 92.4 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 19.71 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.4
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 5.7 / % possible all: 60.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PSZ

1psz


Resolution: 1.65→19.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.9446 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.094 / SU Rfree Blow DPI: 0.091 / SU Rfree Cruickshank DPI: 0.092
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 2909 5.04 %RANDOM
Rwork0.1491 ---
obs0.1508 57680 92.44 %-
Displacement parametersBiso mean: 22.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.5086 Å2-0.9579 Å20.251 Å2
2--0.2075 Å23.25 Å2
3---0.3012 Å2
Refine analyzeLuzzati coordinate error obs: 0.161 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 16 688 5136
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018958HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0516294HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2556SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes148HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1220HARMONIC5
X-RAY DIFFRACTIONt_it8958HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.3
X-RAY DIFFRACTIONt_other_torsion2.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion602SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10165SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2172 115 4.01 %
Rwork0.1569 2756 -
all0.1594 2871 -
obs--92.44 %
Refinement TLS params.

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

IDL11 (°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)
11.11941.08460.6730.3832-0.06770.1034-0.18460.1541-0.2576-0.08030.0986-0.20350.16790.05430.086-0.00010.02190.0783-0.0389-0.01260.01347.8182-18.364235.7485
21.95361.14110.90782.1035-1.56020.0152-0.04070.236-0.1723-0.1374-0.0461-0.19240.01150.00080.0868-0.01380.04430.0501-0.01080.0054-0.010915.5063-16.993337.2955
33.5757-1.828-0.15213.0822-1.17441.349-0.09230.0714-0.1251-0.21730.02930.03960.1686-0.06820.0630.0206-0.00520.0312-0.0322-0.0237-0.04772.3178-13.756630.384
43.99770.06665.61535.7016-5.03743.5489-0.1926-0.0712-0.0792-0.10270.0485-0.19010.3775-0.31230.1441-0.017-0.0970.05580.0069-0.0845-0.0778-5.0291-17.816727.5318
5-1.2816-4.24683.5962-2.39351.95164.4578-0.2047-0.0614-0.022-0.440.1972-0.14490.18210.08070.00750.1019-0.03850.0866-0.0184-0.01590.0437-0.0574-26.176430.3721
60.21410.56430.03480.45630.07080.8701-0.11180.0469-0.22710.1717-0.07660.0510.2037-0.00360.18840.0387-0.00030.06370.0019-0.01450.0429-1.2425-16.631440.1638
73.9247-0.51-0.64482.7978-3.16965.9775-0.06460.3092-0.4499-0.1530.01980.21220.19-0.41780.0448-0.0387-0.03770.0661-0.0343-0.05260.0085-7.398-21.045437.1993
8-0.73933.12491.36435.2595-0.0914-0.36190.1114-0.1556-0.3766-0.0292-0.08640.02330.0686-0.2315-0.0250.07980.01220.0819-0.03560.00090.1186-2.0099-27.263844.8438
91.394-0.6709-0.62251.46740.10950.6476-0.1499-0.152-0.16410.10210.0893-0.00530.10960.00250.0606-0.05560.01670.0339-0.07970.0126-0.105-2.5674-8.561248.3949
103.3-0.1134-2.3302-0.19340.38194.7998-0.27830.1331-0.03740.39170.097-0.07410.6141-0.21620.18140.0389-0.00390.0686-0.07780.0013-0.0629-9.958-6.011150.3759
111.1849-0.1519-0.1370.57050.4270.8536-0.1368-0.1247-0.10140.12620.0673-0.04720.11550.10.0695-0.00330.03020.038-0.00770.0234-0.00799.8388-13.17845.5885
121.1719-2.2308-0.18314.95320.42250.5973-0.1321-0.08180.16760.02350.1892-0.5367-0.00080.1798-0.0571-0.03540.0122-0.00390.0411-0.01190.051317.3419-1.194544.864
13-0.0094-0.67750.45640.9189-0.4381.087-0.0876-0.12010.00610.02980.0593-0.1847-0.1441-0.02130.0283-0.0322-0.00580.0011-0.06440.0055-0.05560.13339.423440.8853
142.8972-0.85371.79431.0032-0.10981.6344-0.0557-0.1798-0.2170.08860.1578-0.0383-0.1139-0.1274-0.1021-0.029-0.01720.0049-0.02880.0127-0.0359-1.42577.712542.6895
154.98040.69861.627710.24270.47172.5316-0.0424-0.0616-0.3148-0.1734-0.01340.71160.0009-0.19620.0558-0.02740.0080.0130.0070.02360.0538-14.19348.323234.7703
165.06631.16790.43224.6641.23310.4887-0.2687-0.08670.56730.06850.08070.33960.0304-0.10280.1880.08540.0196-0.014-0.01170.00480.0133-5.657721.030439.1727
171.5146-0.14321.02591.3115-0.09031.6206-0.04860.1143-0.0662-0.24920.0617-0.0498-0.190.0683-0.01320.0233-0.00150.0051-0.06180.0113-0.0791-4.456811.220128.4973
180.1621-0.4594-0.41960.80541.31021.05470.0480.09930.0178-0.2596-0.0579-0.0897-0.15820.0980.0098-0.0277-0.03490.0214-0.05060.0119-0.05233.33617.588130.7042
190.3557-2.825-1.1432-1.08591.72456.8293-0.00360.35360.0626-0.2093-0.1056-0.29070.04920.10740.10920.0711-0.03380.05940.10260.031-0.027312.4754-3.516924.7748
200.95-1.8796-0.1274.80821.37432.20970.04750.06440.1266-0.3116-0.0045-0.2834-0.20690.1087-0.043-0.0039-0.02820.02570.01470.00870.020211.07325.92235.5629
210.2611-1.612-0.17832.41350.30491.0613-0.0676-0.08710.00220.22050.1148-0.3927-0.20230.1008-0.0471-0.0178-0.0257-0.0125-0.0265-0.0157-0.01617.1603-5.025911.7924
223.6373-0.0505-1.4132.5447-0.55871.6254-0.0225-0.14970.0033-0.00770.0117-0.3232-0.15210.16510.0108-0.0099-0.0318-0.0030.0171-0.01440.057714.7119-6.09710.5963
231.78210.5776-0.55863.6095-0.82072.1541-0.1840.16590.02830.1290.2407-0.12880.20640.2216-0.056700.01350.0097-0.0669-0.0154-0.09571.9556-10.684517.7166
240.40865.1967-0.90382.4342-1.4355-1.961-0.08450.1335-0.0966-0.08530.06010.09880.183-0.37570.02440.04-0.0155-0.00310.0024-0.0473-0.0295-7.5832-11.868217.0905
252.00883.6755-1.5198.181-1.10483.012-0.0449-0.06860.10730.2946-0.02170.0415-0.3027-0.04610.06660.04090.0128-0.0107-0.0174-0.0161-0.0304-1.69550.223319.3217
260.383-0.7625-0.59222.42530.04161.34880.0783-0.01560.0067-0.127-0.15410.1799-0.0982-0.13250.0758-0.0041-0.0074-0.003-0.0201-0.0129-0.0402-2.1956-7.177.6383
271.21730.8831-0.77683.5566-0.56833.86040.04980.01540.1468-0.0623-0.04540.2964-0.2702-0.0157-0.00440.02270.014-0.0219-0.0465-0.0053-0.0015-6.2377-0.41018.4992
280.57040.20130.42722.40910.14020.2223-0.13340.13090.041-0.26450.2083-0.0443-0.16490.0736-0.07490.0142-0.02750.0131-0.0440.0027-0.0742-0.2525-10.3167-0.5038
29-0.2818-1.03544.08512.99873.44878.7242-0.0648-0.38510.2336-0.2361-0.08850.3117-0.3709-0.57650.1532-0.01160.0239-0.03570.001-0.02260.005-12.0258-19.9247-3.025
300.6130.2073-0.07271.65690.39240.5796-0.03060.0821-0.0215-0.21920.0988-0.1433-0.10380.0878-0.06820.0155-0.02820.01930.0138-0.00650.01266.5639-14.14881.8343
312.55690.3979-1.18631.27481.33913.6875-0.0020.08280.2672-0.26880.0649-0.5944-0.3680.1594-0.06290.0177-0.06930.0659-0.0238-0.02170.118618.3823-1.9732.3185
320.77241.4526-0.16835.30180.62690.2048-0.0031-0.0599-0.08130.04860.1367-0.66630.11780.162-0.1337-0.0530.00810.0165-0.0206-0.04630.037615.6764-27.63352.3454
33-0.29130.07570.35021.6966-1.2391.1955-0.0410.02630.06050.04540.0494-0.2110.0424-0.0192-0.0084-0.05480.01030.0053-0.06460.0058-0.057-0.5688-33.34346.5201
342.1920.6627-2.2261.0527-0.29663.1020.02160.30130.1596-0.00260.1527-0.05360.0343-0.2842-0.1744-0.03770.02830.0006-0.04330.0127-0.0489-1.8968-30.8464.646
35-1.1491-0.08261.59824.03421.09381.4623-0.0582-0.00870.5792-0.19880.1086-0.0752-0.05030.0216-0.05040.03980.01240.00030.04930.09530.1557-14.122-24.643112.0667
361.8797-1.1252-0.33253.79352.71762.8395-0.04230.1156-0.22210.1636-0.19670.46620.1732-0.3780.23910.0114-0.01860.0261-0.01890.012-0.0134-12.7212-40.1510.8197
371.3880.5547-0.3292.7094-0.07392.0789-0.0463-0.10150.03220.37680.0696-0.09710.18520.0871-0.02330.05890.0281-0.0067-0.07650.0149-0.0886-2.9584-37.546917
38-1.2340.66061.60520.7712-0.73162.2207-0.0268-0.1939-0.06630.2538-0.00340.01280.1718-0.10830.0303-0.00870.0324-0.0224-0.0195-0.0082-0.01364.9597-23.042717.0071
391.11931.19731.0872-0.51551.3673.96670.1142-0.3249-0.19410.46950.0247-0.4095-0.22970.3264-0.13890.05120.0036-0.09610.0334-0.0076-0.009512.5411-19.978118.634
400.80961.2407-0.03376.3960.7710.6382-0.0281-0.084-0.0650.29950.0999-0.42420.18950.1225-0.07180.03470.0461-0.0380.0059-0.02070.03710.5552-31.296211.4401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|32 - 44}
2X-RAY DIFFRACTION2{A|45 - 54}
3X-RAY DIFFRACTION3{A|55 - 67}
4X-RAY DIFFRACTION4{A|68 - 74}
5X-RAY DIFFRACTION5{A|75 - 80}
6X-RAY DIFFRACTION6{A|81 - 97}
7X-RAY DIFFRACTION7{A|98 - 107}
8X-RAY DIFFRACTION8{A|108 - 113}
9X-RAY DIFFRACTION9{A|114 - 130}
10X-RAY DIFFRACTION10{A|131 - 137}
11X-RAY DIFFRACTION11{A|138 - 166}
12X-RAY DIFFRACTION12{A|167 - 196}
13X-RAY DIFFRACTION13{A|197 - 211}
14X-RAY DIFFRACTION14{A|212 - 223}
15X-RAY DIFFRACTION15{A|224 - 240}
16X-RAY DIFFRACTION16{A|241 - 249}
17X-RAY DIFFRACTION17{A|250 - 269}
18X-RAY DIFFRACTION18{A|270 - 283}
19X-RAY DIFFRACTION19{A|284 - 289}
20X-RAY DIFFRACTION20{A|290 - 309}
21X-RAY DIFFRACTION21{B|32 - 44}
22X-RAY DIFFRACTION22{B|45 - 55}
23X-RAY DIFFRACTION23{B|56 - 66}
24X-RAY DIFFRACTION24{B|67 - 70}
25X-RAY DIFFRACTION25{B|71 - 80}
26X-RAY DIFFRACTION26{B|81 - 98}
27X-RAY DIFFRACTION27{B|99 - 112}
28X-RAY DIFFRACTION28{B|113 - 126}
29X-RAY DIFFRACTION29{B|127 - 135}
30X-RAY DIFFRACTION30{B|136 - 160}
31X-RAY DIFFRACTION31{B|161 - 173}
32X-RAY DIFFRACTION32{B|174 - 196}
33X-RAY DIFFRACTION33{B|197 - 210}
34X-RAY DIFFRACTION34{B|211 - 224}
35X-RAY DIFFRACTION35{B|225 - 231}
36X-RAY DIFFRACTION36{B|232 - 246}
37X-RAY DIFFRACTION37{B|247 - 275}
38X-RAY DIFFRACTION38{B|276 - 284}
39X-RAY DIFFRACTION39{B|285 - 292}
40X-RAY DIFFRACTION40{B|293 - 309}

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