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- PDB-8ev2: Dual Modulators -

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Basic information

Entry
Database: PDB / ID: 8ev2
TitleDual Modulators
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsDNA BINDING PROTEIN / ER-alpha / ligand complex / carbonic anhydrase
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / steroid binding / : / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / transcription coactivator binding / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / : / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-LYQ / Chem-WVE / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsTinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Rangarajan, E.S. / Christodoulou, M. ...Tinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Rangarajan, E.S. / Christodoulou, M. / Passarella, D. / Supuran, C. / Nettles, K.W. / Rastelli, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Eur.J.Med.Chem. / Year: 2022
Title: Design, synthesis, biological evaluation and crystal structure determination of dual modulators of carbonic anhydrases and estrogen receptors.
Authors: Tinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Erumbi, R. / Christodoulou, M.S. / Passarella, D. / Supuran, C.T. / ...Authors: Tinivella, A. / Nwachukwu, J.C. / Angeli, A. / Foschi, F. / Benatti, A.L. / Pinzi, L. / Izard, T. / Ferraroni, M. / Erumbi, R. / Christodoulou, M.S. / Passarella, D. / Supuran, C.T. / Nettles, K.W. / Rastelli, G.
History
DepositionOct 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,79012
Polymers61,7594
Non-polymers3,0318
Water1,31573
1
A: Estrogen receptor
C: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3956
Polymers30,8792
Non-polymers1,5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7 kcal/mol
Surface area11090 Å2
MethodPISA
2
B: Estrogen receptor
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3956
Polymers30,8792
Non-polymers1,5154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-10 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.964, 81.769, 58.555
Angle α, β, γ (deg.)90.000, 111.040, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 306 - 548 / Label seq-ID: 9 - 251

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29299.535 Da / Num. of mol.: 2 / Fragment: Ligand binding domain / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical
ChemComp-LYQ / (3~{a}~{R},4~{S},9~{b}~{S})-4-(2-chloranyl-4-oxidanyl-phenyl)-2,3,3~{a},4,5,9~{b}-hexahydro-1~{H}-cyclopenta[c]quinoline-8-sulfonamide


Mass: 378.873 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-WVE / (3aS,4R,9bR)-4-(2-chloro-4-hydroxyphenyl)-2,3,3a,4,5,9b-hexahydro-1H-cyclopenta[c]quinoline-8-sulfonamide


Mass: 378.873 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 20-25% PEG 3350, 200 mM MgCl2, 200 mM NaCl, 0.1 M Hepes pH 7
PH range: 6.5 - 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.008→54.652 Å / Num. obs: 22425 / % possible obs: 92.5 % / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.8
Reflection shellResolution: 2.008→2.231 Å / Num. unique obs: 1121 / CC1/2: 0.544

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 2qzo

2qzo


Resolution: 2.01→54.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.031 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.422 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 1132 5 %RANDOM
Rwork0.1928 ---
obs0.1956 21293 70.63 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 228.67 Å2 / Biso mean: 52.437 Å2 / Biso min: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0.34 Å2
2--0.85 Å20 Å2
3----0.51 Å2
Refinement stepCycle: final / Resolution: 2.01→54.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 200 73 4083
Biso mean--74.53 38.84 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134195
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174007
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.7055704
X-RAY DIFFRACTIONr_angle_other_deg1.2021.6149261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99722.188192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84715765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.271524
X-RAY DIFFRACTIONr_chiral_restr0.1960.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02823
Refine LS restraints NCS

Ens-ID: 1 / Number: 7160 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.01→2.061 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.583 1 -
Rwork0.369 28 -
obs--1.24 %
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)
16.58546.8032-4.98788.4595-8.901914.050.1249-0.1070.44130.5727-0.01330.2198-1.1929-0.0422-0.11160.3252-0.1804-0.12170.3386-0.13670.414316.56121.51732.271
22.08613.54792.40649.15663.75558.00280.3043-0.4172-0.12510.3965-0.61550.62791.019-0.42790.31120.1941-0.0493-0.03210.27220.07570.3751-3.97-0.9534.197
34.54280.1787-0.94312.7027-1.7155.11740.08670.03240.20540.12340.11870.1415-0.324-0.1853-0.20550.02090.01270.0120.0132-0.00480.10850.16511.71525.358
49.4273-2.1538-7.15521.533-0.912111.8236-0.4955-0.3215-0.4262-0.24290.0512-0.0021.43810.2660.44430.40310.0281-0.020.07610.13010.33294.684-6.13429.275
54.92231.1371-1.06625.5787-0.4464.5003-0.1187-0.0766-0.3769-0.3322-0.0941-0.14230.48760.33410.21280.06950.0450.02230.04690.00850.06599.0423.92621.076
64.6110.07240.39352.8025-0.20564.93910.0736-0.35810.1626-0.0322-0.2052-0.146-0.05230.50660.13150.0027-0.00980.00630.11160.02240.056515.69811.08919.641
713.53843.1027-4.13369.0125-5.00413.2523-0.44720.3022-0.5394-1.26420.12420.51590.3281-0.9570.3230.2025-0.021-0.09170.3482-0.00590.3107-10.5768.32618.99
86.38962.34076.78742.7970.94968.68140.33070.4126-0.43060.1104-0.3153-0.77680.46471.2694-0.01540.2540.24490.10380.99080.08610.445933.6956.1591.279
98.5799-0.08631.2694.1569-1.85699.2066-0.3280.25320.5865-0.43210.17670.5337-0.4657-0.9920.15130.3897-0.06980.02610.2945-00.266211.87613.754-15.774
1012.7238-6.13757.3446.9242-2.95289.9873-0.47210.0918-0.18310.09810.28890.20380.4743-0.48050.18320.2347-0.04280.10880.120.03490.126912.0465.314-10.612
113.3976-2.07190.75228.1439-0.97955.09110.01160.0345-0.3134-0.3695-0.2256-0.15090.92240.05550.2140.35070.08180.09920.05020.02560.0816.9951.772-0.177
126.4255-3.0745-2.98726.9529-2.229411.1331-0.3510.2940.658-0.38640.1934-0.2562-1.2318-0.27570.15750.537-0.0159-0.10390.1240.11620.237412.18921.567-8.003
1322.9173-2.475-8.28493.3784-2.597310.84480.18661.19260.7730.00130.21330.3868-0.117-1.3114-0.39990.47190.1733-0.10890.4760.06950.59821.20119.487-8.074
1420.59891.47052.54134.6046-0.33185.2554-0.2134-0.01440.6202-0.0396-0.03690.1992-0.6425-0.32380.25030.33580.08170.02870.03910.03070.16419.2920.3632.156
153.75492.4525-0.303110.7872-1.00466.5448-0.28870.02430.1478-0.4079-0.1073-0.3094-0.01420.89740.3960.11920.01750.02450.13910.060.079222.49311.1263.214
1611.7306-2.58681.16192.71350.01920.15930.138-0.7146-0.58040.0502-0.08020.24330.0701-0.0847-0.05780.39970.02180.05030.25790.04050.2216.42-5.48112.235
175.00463.81120.457210.59333.61017.6667-0.16220.0243-0.2994-0.0019-0.1555-0.48950.3941.1980.31770.04170.09190.08090.38310.13180.257528.7047.39210.525
1813.24875.20755.26755.33422.27927.0087-0.230.1668-0.049-0.35430.11770.1369-0.1658-0.07090.11240.07750.0220.03140.08140.04680.072412.14111.7117.664
1911.6414-0.2392-0.61528.80121.58386.853-0.1967-0.0871-0.41210.50450.24990.53240.2303-0.8844-0.05320.4823-0.11990.0280.2952-0.05570.37013.761-1.626-6.098
2012.11262.8768-0.530812.55490.18860.10810.04820.06160.4083-0.2591-0.08840.4146-0.0261-0.13270.04020.18690.0629-0.00910.2288-0.0330.2918-7.75620.87825.369
2124.2528-10.180415.22494.8287-9.563327.69840.05660.0655-1.0258-0.0660.02110.33060.2667-0.208-0.07770.35620.00410.08680.0289-0.02720.342315.4-7.254-7.62
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 321
2X-RAY DIFFRACTION2A322 - 338
3X-RAY DIFFRACTION3A339 - 394
4X-RAY DIFFRACTION4A395 - 412
5X-RAY DIFFRACTION5A413 - 472
6X-RAY DIFFRACTION6A473 - 531
7X-RAY DIFFRACTION7A532 - 548
8X-RAY DIFFRACTION8B306 - 321
9X-RAY DIFFRACTION9B322 - 338
10X-RAY DIFFRACTION10B339 - 363
11X-RAY DIFFRACTION11B364 - 394
12X-RAY DIFFRACTION12B395 - 407
13X-RAY DIFFRACTION13B408 - 421
14X-RAY DIFFRACTION14B422 - 438
15X-RAY DIFFRACTION15B439 - 455
16X-RAY DIFFRACTION16B456 - 469
17X-RAY DIFFRACTION17B470 - 496
18X-RAY DIFFRACTION18B497 - 531
19X-RAY DIFFRACTION19B536 - 548
20X-RAY DIFFRACTION20C568 - 576
21X-RAY DIFFRACTION21D569 - 574

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