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- PDB-3hh2: Crystal structure of the myostatin:follistatin 288 complex -

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Basic information

Entry
Database: PDB / ID: 3hh2
TitleCrystal structure of the myostatin:follistatin 288 complex
Components
  • Follistatin
  • Growth/differentiation factor 8
KeywordsSIGNALING PROTEIN/CYTOKINE / protein-protein complex / TB domain / cystine knot motif / TGF-beta fold / disulfide linked dimer / follistatin domain (FSD) / Cleavage on pair of basic residues / Cytokine / Disulfide bond / Glycoprotein / Growth factor / Secreted / SIGNALING PROTEIN-CYTOKINE COMPLEX
Function / homology
Function and homology information


negative regulation of muscle hypertrophy / activin receptor antagonist activity / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / skeletal muscle satellite cell differentiation / negative regulation of satellite cell differentiation / Antagonism of Activin by Follistatin / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / ameloblast differentiation ...negative regulation of muscle hypertrophy / activin receptor antagonist activity / negative regulation of skeletal muscle tissue growth / negative regulation of myoblast proliferation / skeletal muscle satellite cell differentiation / negative regulation of satellite cell differentiation / Antagonism of Activin by Follistatin / myoblast migration involved in skeletal muscle regeneration / negative regulation of skeletal muscle satellite cell proliferation / ameloblast differentiation / skeletal muscle atrophy / ovulation cycle process / positive regulation of hair follicle development / response to gravity / regulation of BMP signaling pathway / gamete generation / skeletal muscle tissue regeneration / pattern specification process / activin binding / negative regulation of activin receptor signaling pathway / negative regulation of myoblast differentiation / heparan sulfate proteoglycan binding / response to muscle activity / negative regulation of epithelial cell differentiation / negative regulation of kinase activity / hair follicle morphogenesis / muscle cell cellular homeostasis / positive regulation of macrophage chemotaxis / female gonad development / response to testosterone / odontogenesis of dentin-containing tooth / keratinocyte proliferation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / BMP signaling pathway / hematopoietic progenitor cell differentiation / positive regulation of lamellipodium assembly / response to electrical stimulus / negative regulation of insulin receptor signaling pathway / cellular response to dexamethasone stimulus / transforming growth factor beta receptor signaling pathway / skeletal system development / cytokine activity / growth factor activity / response to organic cyclic compound / response to estrogen / heparin binding / cellular response to hypoxia / response to ethanol / cell differentiation / signaling receptor binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like ...Follistatin, N-terminal / Extracellular Matrix Fibrillin / TGF-beta binding (TB) domain / Follistatin/Osteonectin EGF domain / Follistatin/Osteonectin-like EGF domain / TB domain / TGF-beta binding (TB) domain profile. / TGF-beta binding (TB) domain superfamily / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Kazal type serine protease inhibitors / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Kazal domain superfamily / Transforming growth factor beta like domain / TGF-beta family profile. / Kazal domain / Kazal domain profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Cystine-knot cytokine / Ribbon / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Growth/differentiation factor 8 / Follistatin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsCash, J.N. / Thompson, T.B.
CitationJournal: Embo J. / Year: 2009
Title: The structure of myostatin:follistatin 288: insights into receptor utilization and heparin binding
Authors: Cash, J.N. / Rejon, C.A. / McPherron, A.C. / Bernard, D.J. / Thompson, T.B.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Growth/differentiation factor 8
B: Growth/differentiation factor 8
C: Follistatin
D: Follistatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6989
Polymers88,0294
Non-polymers6695
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-66.7 kcal/mol
Surface area39490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.634, 59.540, 286.126
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a heterotetramer (dimer of dimers).

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Components

#1: Protein Growth/differentiation factor 8 / GDF-8 / Myostatin


Mass: 12422.212 Da / Num. of mol.: 2 / Fragment: UNP residues 268-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mstn, Gdf8 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O08689
#2: Protein Follistatin / FS / Activin-binding protein


Mass: 31592.205 Da / Num. of mol.: 2 / Fragment: UNP residues 30-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FST / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P19883
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: PEG 1000, Ethanol, Phosphate/citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 53203 / % possible obs: 98.7 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.098 / Χ2: 1.016 / Net I/σ(I): 16.536
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.235.50.42747051.008188.9
2.23-2.3270.42252140.982199
2.32-2.428.40.35753200.9951100
2.42-2.559.50.30753050.9981100
2.55-2.719.80.22153640.9011100
2.71-2.929.80.16753311.0631100
2.92-3.219.80.12653671.0571100
3.21-3.689.80.09654101.0941100
3.68-4.639.60.07654821.045199.9
4.63-508.90.0657050.992199.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å28.96 Å
Translation3 Å28.96 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMAC5.4.0077refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→28.96 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.798 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2702 5.1 %RANDOM
Rwork0.208 ---
obs0.21 53005 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.37 Å2 / Biso mean: 25.35 Å2 / Biso min: 3.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 41 349 6208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226068
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9598243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2645778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.30923.871248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.834151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6871539
X-RAY DIFFRACTIONr_chiral_restr0.070.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214567
X-RAY DIFFRACTIONr_mcbond_it2.11323846
X-RAY DIFFRACTIONr_mcangle_it3.29236159
X-RAY DIFFRACTIONr_scbond_it2.87322222
X-RAY DIFFRACTIONr_scangle_it4.03932076
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 154 -
Rwork0.267 3191 -
all-3345 -
obs--85.33 %
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)
15.0453-2.36981.28716.0654-2.96957.93730.0158-0.13530.3399-0.2676-0.1849-0.3141-0.32420.38280.16910.1832-0.03250.00170.12820.04110.2247-18.4249-1.934829.6109
21.9355-0.7361.10571.7981-3.582612.0328-0.0732-0.20240.18580.2176-0.0624-0.0445-0.51640.42370.13560.1731-0.0054-0.01410.1237-0.0170.1866-17.9295-2.319947.3989
32.8517-0.327-1.29024.8394-2.04282.8092-0.17750.05770.064-0.04690.29910.3987-0.3815-0.2145-0.12160.14990.0331-0.03440.1526-0.02770.1784-18.3751-8.157158.4662
43.5639-0.2193.29322.0549-1.04926.0065-0.1773-0.15780.28190.1498-0.0242-0.088-0.4777-0.11260.20150.17760.01660.00830.1163-0.01850.1935-17.8506-4.469443.4909
53.47470.8152-1.47195.8322-0.06462.6920.02510.07140.3284-0.21030.07950.2068-0.0375-0.2343-0.10460.16680.0212-0.02880.16680.0130.1673-29.3078-15.395523.109
66.5495-1.72360.901710.714910.364311.07730.12970.02410.265-0.2098-0.22370.4345-0.6103-0.19130.0940.13690.00190.00050.21440.04130.2528-41.6458-17.289326.239
79.9433-4.05735.98435.4633-1.18427.81720.0765-0.1204-0.0498-0.17960.00980.33250.0216-0.3006-0.08630.1949-0.02050.02960.15690.03650.1637-25.1914-12.507632.9771
81.7189-0.18870.58732.14490.41414.5014-0.0217-0.09810.06370.099-0.0053-0.0307-0.0679-0.06290.02690.13470.0327-0.01640.1773-0.02070.2086-13.7316-16.283956.9248
90.7938-0.76711.87231.0128-2.21548.41660.1650.0662-0.0253-0.1573-0.03270.03990.2980.2701-0.13230.17190.0135-0.00480.1428-0.00610.1753-15.6461-14.697244.3777
102.0472-0.5772-3.72475.23953.58378.041-0.1080.101-0.2585-0.0019-0.39260.52680.5306-0.76420.50060.1143-0.01580.07350.2601-0.04890.2425-41.4588-26.112740.1591
112.0241-0.4624-0.31621.94832.30957.7732-0.07120.1430.01530.017-0.19540.31130.0182-0.38060.26670.10620.00030.0150.1781-0.00930.2133-38.4746-25.041429.8832
126.7131-0.2231-0.31730.3807-1.11333.39910.12060.20480.5865-0.1081-0.14610.3168-0.3448-0.47950.02560.16160.0156-0.00050.1806-0.02030.1459-32.3872-26.860812.2181
133.6979-1.9758-2.61335.82844.15458.5702-0.08880.3774-0.2112-0.1317-0.14560.2970.1712-0.48790.23430.1136-0.0119-0.0020.2152-0.00670.1772-36.4119-29.324723.4909
145.78554.04314.68213.17354.47747.9643-0.1162-0.06040.3329-0.0506-0.28010.3213-0.4314-0.35290.39630.11360.05460.0280.16660.00020.1959-35.359-14.874145.2926
158.7450.5929-0.77112.6645-4.22971.45030.05210.06260.0621-0.0953-0.03010.08230.0305-0.0537-0.02190.17550.0008-0.00430.2044-0.01140.1628-24.3154-12.565445.8434
161.64830.05930.19689.79354.9443.1167-0.11540.09130.5676-0.51260.15470.4704-0.3197-0.1869-0.03930.22040.00170.01590.2246-0.00410.2788-27.6135-1.891143.3729
171.9899-1.391-2.74573.36885.45959.08930.0504-0.10510.1396-0.0850.02670.0339-0.12640.0946-0.07710.17750.01360.01090.18880.00770.208-28.1723-24.582630.8948
181.5191-1.2004-2.28661.24262.1346.0796-0.0122-0.08470.0384-0.01850.10690.02570.02010.2779-0.09470.169-0.0103-0.00780.1775-0.01040.1814-24.9635-28.794220.0035
192.28860.78360.78773.12560.42364.05970.0515-0.0423-0.00560.1024-0.02270.29510.2136-0.2616-0.02880.11580.00340.02840.188-0.00470.1863-35.6731-26.480154.0172
203.65072.47620.44363.19860.23391.32140.0422-0.15190.23750.3182-0.05940.2427-0.0659-0.17190.01720.12670.0340.01320.1794-0.02960.14-28.6115-20.44658.9055
214.7127-1.32640.83995.1442-1.29779.63840.15650.4101-0.4404-0.2179-0.1180.60760.5704-0.2943-0.03850.2583-0.03690.01720.1975-0.03650.1692-38.37-42.1547.5864
220.1944-0.7101-1.10982.60243.89049.54660.0008-0.0114-0.10180.1024-0.08920.19130.148-0.24380.08840.2383-0.0355-0.00650.1799-0.00570.18-34.2213-48.526638.3788
233.1029-1.44670.50147.1695-0.25924.0777-0.064-0.11310.20750.2885-0.00930.0477-0.2956-0.16240.07340.24940.0179-0.04240.11230.00290.1416-29.2974-45.76626.4492
243.24251.4553-0.73383.3059-0.30412.0685-0.12270.0935-0.1355-0.08220.1373-0.11650.2364-0.0702-0.01470.21190.02790.00030.1357-0.01320.139-26.2578-46.824411.2933
257.01122.3849-1.77587.621-5.14873.48280.0674-0.12260.036-0.32190.48671.19160.0112-1.0299-0.55410.13570.1414-0.02060.38050.02660.1232-34.8252-27.836-1.3119
262.66830.123-0.34352.5702-1.49474.5419-0.03330.11620.2137-0.21670.04210.033-0.1691-0.187-0.00890.22270.0451-0.02130.1966-0.00450.1157-21.9734-28.5262-5.5951
273.062-0.4239-0.00933.86611.79582.52910.1197-0.37630.24740.3113-0.07-0.2168-0.04320.104-0.04960.2152-0.00410.01950.175-0.02180.1071-8.9401-26.7307-0.2736
285.7409-0.8970.1385.91990.55795.19990.1714-0.40.10080.7592-0.0151-0.25410.30880.0496-0.15630.2137-0.0169-0.06230.1267-0.01990.1175-1.8763-31.55872.745
2911.4829-3.63692.30581.1991-1.3939.7655-0.2121-0.3243-0.48640.14160.382-0.96460.47550.7563-0.16980.4141-0.0446-0.07720.09680.01580.29250.9484-41.57514.8269
303.03271.52340.84253.6050.44312.4509-0.10920.27870.249-0.05390.10930.2041-0.27750.11-0.00010.17790.02050.01030.14960.04340.1499-17.3913-11.068714.442
316.1555-0.8245-0.8192.7629-0.736912.2047-0.3301-0.20860.37640.26-0.0041-0.1493-0.25760.25720.33410.2428-0.0184-0.01860.21990.0260.2052-0.7928-4.199323.3471
320.2413-0.1036-0.96161.77953.55439.5209-0.2112-0.02930.407-0.2944-0.2344-0.3535-1.28930.49010.44560.3009-0.1705-0.04910.14080.06520.24677.4763-2.281641.1505
336.1944-0.74190.56593.0062-1.03059.372-0.11020.3532-0.0023-0.1858-0.07310.1292-0.3181-0.04020.18330.06270.0090.00250.1767-0.0470.1853.0274-10.260645.2714
342.40570.8841-0.9022.489-1.23114.16670.1117-0.0743-0.01290.177-0.168-0.3143-0.23040.30140.05630.06380.0191-0.03350.1804-0.0180.20381.2962-11.884359.3432
356.8884-2.0937-5.27459.1959-0.60234.6070.7208-0.20481.1462-0.00830.2457-0.3609-0.5857-0.1799-0.96650.29760.1139-0.03180.1788-0.10350.0651-17.8597-5.474872.8005
361.7468-0.0943-1.76371.84580.28292.91260.0608-0.1530.09830.0875-0.0667-0.0223-0.35-0.01280.0060.18830.0441-0.02950.1892-0.03050.1111-14.4073-14.809574.965
373.6852-1.26252.62444.29291.44069.7871-0.0316-0.2705-0.33280.1983-0.00510.34920.0049-0.82560.03670.15760.00540.04750.2540.05130.1168-23.6289-27.645179.9363
381.9779-1.15021.0682.5053-1.10440.70390.23480.3036-0.2948-0.3182-0.11290.00430.20780.2931-0.12190.13330.0587-0.03130.2344-0.01560.1175-13.9692-33.283570.8552
394.8707-1.9248-1.12346.58753.52498.91990.11480.4625-0.0115-0.4970.00820.00210.0515-0.0255-0.1230.19240.0449-0.05270.17630.01230.2096-15.3022-36.948667.5641
407.9946-1.6771-2.092214.69125.226614.85390.26920.4306-0.5381-0.4823-0.3159-0.4576-0.02051.10780.04670.14850.03370.04510.37990.02170.2317-3.6187-36.96666.0799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 25
3X-RAY DIFFRACTION3A26 - 34
4X-RAY DIFFRACTION4A35 - 47
5X-RAY DIFFRACTION5A48 - 62
6X-RAY DIFFRACTION6A63 - 70
7X-RAY DIFFRACTION7A71 - 78
8X-RAY DIFFRACTION8A79 - 92
9X-RAY DIFFRACTION9A93 - 109
10X-RAY DIFFRACTION10B1 - 13
11X-RAY DIFFRACTION11B14 - 24
12X-RAY DIFFRACTION12B25 - 34
13X-RAY DIFFRACTION13B35 - 43
14X-RAY DIFFRACTION14B44 - 53
15X-RAY DIFFRACTION15B54 - 60
16X-RAY DIFFRACTION16B61 - 71
17X-RAY DIFFRACTION17B72 - 84
18X-RAY DIFFRACTION18B85 - 109
19X-RAY DIFFRACTION19C1 - 37
20X-RAY DIFFRACTION20C38 - 63
21X-RAY DIFFRACTION21C64 - 79
22X-RAY DIFFRACTION22C80 - 99
23X-RAY DIFFRACTION23C100 - 128
24X-RAY DIFFRACTION24C129 - 162
25X-RAY DIFFRACTION25C163 - 177
26X-RAY DIFFRACTION26C178 - 222
27X-RAY DIFFRACTION27C223 - 253
28X-RAY DIFFRACTION28C254 - 280
29X-RAY DIFFRACTION29C281 - 288
30X-RAY DIFFRACTION30D1 - 63
31X-RAY DIFFRACTION31D64 - 86
32X-RAY DIFFRACTION32D87 - 99
33X-RAY DIFFRACTION33D100 - 124
34X-RAY DIFFRACTION34D125 - 162
35X-RAY DIFFRACTION35D163 - 177
36X-RAY DIFFRACTION36D178 - 211
37X-RAY DIFFRACTION37D212 - 227
38X-RAY DIFFRACTION38D228 - 261
39X-RAY DIFFRACTION39D262 - 279
40X-RAY DIFFRACTION40D280 - 287

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