8q6o

X. laevis CMG dimer bound to dimeric DONSON - without ATPase

Method: ELECTRON MICROSCOPY D_max: 218.9 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8q6o
沉积日期 deposition_date	2023-08-14
结构标题 title	X. laevis CMG dimer bound to dimeric DONSON - without ATPase
关键词 keywords	DNA replication initiation, Xenopus egg extract, primordial dwarfism, replicative helicase, genome stability, REPLICATION; REPLICATION
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	67.34 Å
回转半径 Rg (电子) rg_electron	67.13 Å
零角强度 I(0) i0	7614650000.00
分子量 molecular_weight	740660.0 kDa
排除体积 excluded_volume	927860 Å³
包络体积 envelope_volume	1477200 Å³
水化壳体积 shell_volume	179020 Å³
包络直径 envelope_diameter	232.5 Å
壳层 Rg shell_rg	72.40 Å
包络 Rg envelope_rg	64.26 Å
形状 Rg shape_rg	67.17 Å
总 Rg total_rg	67.07 Å
总原子数 total_atoms	51983
残基数 n_residues	6454
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	218.9 Å
Rg (实空间) rg_real	67.12 Å
Rg 误差 (实空间) rg_real_error	2.18 Å
I(0) (实空间) i0_real	7.6150e+09
I(0) 误差 (实空间) i0_real_error	1.4930e+08
Rg (倒空间) rg_reciprocal	68.02 Å
I(0) (倒空间) i0_reciprocal	7627000000.0000
解质量估计 total_estimate	0.8678
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	85.6 Å
偏度 Skewness skewness	0.129
峰度 Kurtosis kurtosis	-0.421
角度范围 angular_range	— – 0.1150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	505400000.0000
实空间数据点数 n_real_points	24
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.736

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (13)

Entity 1 polymer

描述 description	DNA replication licensing factor mcm2
分子量 formula_weight	100397.6 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,2
原子数 atom_count	51983

MADSSESFNIATSPRAGSRRDALTSSPGRDLPPFEDESEGMFGDGVVPEEEEDGEELIGDAMERDYRPISELDRYEVEGLDDEEDVEDLTASQREAAEQSMRMRDREMGRELGRMRRGLLYDSDEEEEDRPARKRRMAERAAEGAPEEDEEMIESIENLEDMKGHTVREWVSMAATRLEIYHRFKNFLRTHVDEHGHNVFKEKISDMCKENKESLPVNYEDLAAREHVLAYFLPEAPAEMLKIFDEAAKEVVLVMYPKYDRIAREIHVRISHLPLVEELRSLRQLHLNQLIRTSGVVTCCTGVLPQLSMVKYNCNKCNFILGPFFQSQNQEVRPGSCPECQSFGPFEINMEETVYQNYQRITIQESPGKVAAGRLPRSKDAILLADLVDSCKPGDEIELTGIYHNNYDGSLNTANGFPVFATVILANHITKKDDKVAVGELTDEDVKAIVALSKDERIGERIFASIAPSIYGHEDIKRGLALALFGGEAKNPGGKHKVRGDINVLLCGDPGTAKSQFLKYVEKVASRAVFTTGQGASAVGLTAYVQRHPVTKEWTLEAGALVLADRGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCTVIAASNPIGGRYDPSLTFSENVDLTEPIVSRFDILCVVRDTVDPVQDEMLARFVVSSHIKHHPSSKDIANGDAAEFALPNTFGVEALPQEVLKKYIMYAKEKIRPKLNQMDQDKVAKMYSDLRKESMATGSIPITVRHIESMIRMAEAHARMHLRDYVVEDDVNMAIRVMLESFIDTQKFSVMRSMRKTFARYLAFRRDNNELLLFVLKQLIAEQVTYQRNRYGAQQDTIEVPEKDLVDKARQINIHNLSAFYDSDLFKMNKFTHDVKKKLIIQQF

Entity 2 polymer

描述 description	Maternal DNA replication licensing factor mcm3
分子量 formula_weight	90536.5 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,3

MDYGGGFEDHELREAQREYLDFLDDDQDQGLYHGKVRDMIGSNEHRLIVNLNDVRRKNDKRANLMLNDAFAETIAFQRALKDLVASIDATYAKQFEEFSVGFEGSFGSKHVSPRTLTASLLGSLVCVEGIVTKCSLVRPKVMRSVHYCPATKKTLERKYSDLTSLEAFPSSSIYPTKDEENNPLETEYGLSTYKDHQTLSIQEMPEKAPAGQLPRSVDIIADDDLVDKCKPGDRVQIVGIYRCLPSKQGGFTSGTFRTILLANNIKLMSKEIAPTFSADDVAKIKKFCKAHSKDIFEHLSKSLAPSIHGHEYIKKAILCMLLGGNEKVLENGTRIRGDINVLLIGDPSVAKSQLLRYVLHTAPRAIPTTGRGSSGVGLTAAVTTDQETGERRLEAGAMVLADRGVVCIDEFDKMSDMDRTAIHEVMEQGRVTIAKAGIQARLNARCSVLAAANPVYGRYDQYRTPMENIGLQDSLLSRFDLLFIVLDKMDADNDQEIADHVLRMHRYRTPGEQDGYALPLGCSVEIFATDDPNASDVTDQELQIYEKHDNLLHGPRKNKSKIVSMQFIRKYIHVAKLIKPVLTSEAADYISQEYAKIRNHDQINNDSARTMPVTARALETMIRLSTAHAKVRMSKTIERQDAETALELVQFAYFKKVLAKEKKKTDKDLHDENLSQDTLSQESVRKSSRRAGKIADSQDDSMDPYSFSEQDSSLNENLSQSLRPQRKKAESQDGKRSLSQNRTKEFKAALLKAFKSSRSQSVAVSQLLELINKGNPEPFERSEVKEALDNMQNDNQVMVSEDVVFLI

Entity 3 polymer

描述 description	DNA replication licensing factor mcm4-B
分子量 formula_weight	97256.3 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,4

MSSPTSTPSRRRNKRGRGSNPPTPHGEEVQSPPSQRRRTEDSTSIGELLPMPTSPSGDVQSPSGQELLFSSPAPSRHSAHQSELDLSSPLTYGTPSSRVEGTPRSGIRGTPARQRPDLGSARKVKQVDLHSDQPAAEELVTSEQSLGQKLVIWGTDVNVATCKEKFQRFVQRFIDPSAKEEDNVGLDLNEPIYMQRLEEINVVGDPFLNIDCDHLRNFDQDLYRQLVCYPQEVIPTFDMAANEIFFERYPDSILEHQIQVRPYNALKTRNMRSLNPEDIDQLITISGMVIRTSQIIPEMQEAFFKCQVCAFTTRVEIDRGRIAEPSVCKHCNTTHSMALIHNRSMFSDKQMIKLQESPEDMPAGQTPHTTILYGHNDLVDKVQPGDRVNVTGIYRAVPIRVNPRVRNVKSVYKTHIDVIHYRKTDSKRLHGIDEDTEQKLFTEERVAMLKELAAKPDIYERLAAALAPSIYEHEDIKKGILLQLFGGTRKDFSHTGRGKFRAEVNILLCGDPGTSKSQLLQYVFNLVPRGQYTSGKGSSAVGLTAYVMKDPETRQLVLQTGALVLSDNGICCIDEFDKMNESTRSVLHEVMEQQTLSIAKAGIICQLNARTSVLAAANPVESQWNPKKTTIENIQLPHTLLSRFDLIFLMLDPQDEAYDRRLAHHLVALYYQSEEQMKEEHLDMAVLKDYIAYARTYVNPRLSEEASQALIEAYVSMRKIGSGRGMVSAYPRQLESLIRLSEAHAKVRFSNKVETIDVEEAKRLHREALKQSATDPRTGIVDISILTTGMSATARKRKEELAQVLKKLIQSKGKTPALKYQQLFEDLRGQSDAAITKDMFDEALHALADDDYLTVTGKTVRLL

Entity 4 polymer

描述 description	DNA replication licensing factor mcm5-A
分子量 formula_weight	82556.4 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,5

MSGFDDLGVYYSDSFGGEQQVGDDGQAKKSQLKKRFREFLRQYRIGTDRTGFTFKYRDELKRHYNLGEYWIEVEMEDLASFDEDLADYLYKQPTEHLQLLEEAAQEVADEVTRPRPAGEETIQEIQVMLRSDANPANIRSLKSEQMSHLVKIPGIIIAATAVRAKATKISIQCRSCRNTIGNIAVRPGLEGYAMPRKCNTEQAGRPNCPLDPYFIIPDKCKCVDFQTLKLQESPDAVPHGELPRHMQLYCDRYLCDKVVPGNRVTIMGIYSIRKSGKTSTKGRDRVGVGIRSSYIRVVGIQVDTEGTGRSAAGAITPQEEEEFRRLAAKPDIYETVAKSIAPSIYGSSDIKKAIACLLFGGSRKRLPDGLTRRGDVNLLMLGDPGTAKSQLLKFVERCSPIGVYTSGKGSSAAGLTASVMRDPVSRNFIMEGGAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRCSVLAAANSVYGRWDDTKGEENIDFMPTILSRFDMIFIVKDEHNEQRDMTLAKHVMNVHLSARTQSSSVEGEVDLNTLKKYIAYCRAKCGPRLSAEAAEKLKNRYILMRSGAREHERETEKRSSIPITVRQLEAIVRISESLGKMKLQPFATETDVEEALRLFQVSTLDAAMSGSLSGVEGFTTQEDQEMLSRIEKQMKKRFAIGSQVSEHSIIQDFLKQKYPEHAIHKVLSLMMRRGEIQHRLQRKVLYRIK

Entity 5 polymer

描述 description	Maternal DNA replication licensing factor mcm6
分子量 formula_weight	92753.0 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,6

MELGGPAAAGDTDIAGQQLFKDELSDKCQKLFLEFLEECKGKDGSNLYVSAAEELIRPERNTLAVNFTDIEYYNQQLATTIQEEYYRVYPHLCRAVRSFARQMGNIPANKEFYIAFSDFPARQKIRELSSAKIGTLLRISGQVVRTHPVHPELVSGTFLCMDCQSIVKDVEQQFRYTQPTICKNPVCANRRRFTLDTNKSRFVDFQKVRIQETQAELPRGAIPRSVEIILRAEAVESAMAGDRCDFTGTLIVVPDVSALAAGDARMETGAKVTGGEGFNSEGVQGLKALGVRDLSYRLAFLACYVGATNPRFGGKDLREEDQTAESIKNQMTVQEWEKVFEMSQDKNLYHNLCTSLFPTIHGNDEIKRGVLLMLFGGVPKTTMEGTSLRGDINVCIVGDPSTSKSQFLKHVEEFSPRAVYTSGKASSAAGLTAAVVKDEESHEFVIEAGALMLADNGVCCIDEFDKMDLKDQVAIHEAMEQQTISITKAGVKATLNARTSILAAANPVGGRYERSKSLKHNVNLSAPIMSRFDLFFILVDECNEVTDYAIARRIVDLHARNEESIERVYSIEDIQRYLLFARQFQPKITKEAEEFIVEQYRRLRQRDGSGVAKSSWRITVRQLESLIRLSESMARMHCSDEVQPKHVKEAFRLLSKSIIRVDTPDVSFDQGEDEKNIEGENNGNLNNGEEAMETNQDEPINEKPSSNAGLKMSFAEYKQISNLLVLYMQKMEETEEECHLTTTDLVNWYLKEMEAEIETETELILKKRLIEKVIHRLIYYDHILIELNKSELKTMDDTKETGEDAAEDRILVVNPNYMLED

Entity 6 polymer

描述 description	DNA replication licensing factor mcm7-B
分子量 formula_weight	81841.5 kDa
EC 编号 ec_number	3.6.4.12
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F,7

MPRDYQAEKEKCKTFLQEFYKDDEFGKKNFKYGVQLANIAHREQVALCIDLDDLAEEDPELVDAICENTRRYTNLFADAVQELLPQYKEREVVHKDALDVYIEHRLMMEQRGRDPNEMRDPHNQYPPELMRRFELYFKAPSSSKARVVRDVKADSIGKLVTVRGIVTRVTEVKPMMVVATYTCDQCGAETYQPIQSPTFMPLIMCPSRECQTNRSGGRLYLQTRGSKFIKFQELKIQEHSDQVPVGNIPRCMSVYVRGENTRLAQPGDHVGITGVFLPMLRTGFRQVVQGLLSETYLESHRLVKMNKTEDDELGTEELSEEELRQITEEDFYEKLAASIAPEIYGHEDVKKALLLLLVGGVDHSPRGMKIRGNINVCLMGDPGVAKSQLLSYIDRLAPRSQYTTGRGSSGVGLTAAVMKDPVTGEMTLEGGALVLADQGVCCIDEFDKMMDSDRTAIHEVMEQQTISIAKAGIMTTLNARCSILAAANPAYGRYNPKKTVEQNIQLPAALLSRFDLLWLIQDKPDRDNDLRLAQHITYVHQHSKQPPSQFQPMDMKLMRRYITMCKSKQPAIPESLADYLTAAYVEMRKEARTNKDMTFTSARTLLSILRLSTALARLRLEDVVEKEDVNEAMRLTEMSKDSLQGDKGHASRTQRPADVIFSTIREMVPEKGARSVKYSEAEQRCVSKGFTPAQFEAALEEYEELNVWLVNQARTKITFV

Entity 7 polymer

描述 description	DNA replication complex GINS protein PSF1
分子量 formula_weight	23171.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	M,G

MFCEKAIELIRELQRASDGQLPAFNEDGIRQILEEMKALYEQNQADVNEAKTEGRSDLIPTIKFRHCCLLRNRRCIVAYLYDRLLRIRALRWEYGSVLPSALRFHMSTEEMDWFNQYKRSLATYMRSLGGEEGLDITQDMKPPKSLYIEVRCLRDYGEFEIDDGTTILLKKNSQHFLPRWKCEQLIRQGVLEHVLS

Entity 8 polymer

描述 description	DNA replication complex GINS protein PSF2
分子量 formula_weight	21348.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	N,H

MDASEVEFLAEKEQVTVIPNFSLDKVYLIGGDLGPFNPSLPVEVPLWLAINLKQRQKCRIVPPEWMDVEKLEAIRDQERREETFTPMPSPYYMELTKLLLNHAADNIPKADEIRTLVKDTWDTRIAKLRLSADSFVKGQEAHAKLDNLTLMEINTIGTFFTESLNHMYKLRTSLQNPEEGQSQDY

Entity 9 polymer

描述 description	DNA replication complex GINS protein PSF3
分子量 formula_weight	23948.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	O,I

MWEPYMPVEPGLGREENFLSLEDLLMSQEKLPCCIESGFPRLGFLDKGGDSDSIPEGSKMELPLWLAKGLYDNKRRVLSVELPKIYREGWRTVFSADANVVDLHKMGPHYYGFGSQLLNFDSPENPEIAKTILQTFVGRFRRIMDSSQNAYNEDTSGLVARLDELERSLFRAGQRGLNAFQSWERGKAAQITASNLVQNYKKRKFNEADA

Entity 10 polymer

描述 description	Cell division control protein 45 homolog
分子量 formula_weight	65695.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	P,J

MFVSDLRKEFFDVIVTERVLLLVAPDVDALCACKILQALFQCDHVQYTLVPVSGWQELETLFLEHKEQFRYFVLINCGANIDLLETLQPQEEAIFYICDTHRPIDVVNIYNDSQVKLLIRQDDDLEIPAYDDIFNDDEEDGEDSGNESDGAEPSGKRRRFDEAAVERRIERRRQRREWEARRREIIFDYEQYEYHGTSSAMMMFELAWIMSKDSNDMLWWAIVGLTDQWVQDRITQMKYVTDVGTLQRHVSRHNHRNEDEENSLSIDCMRIAFEYDLRLSLYQHWSLYESICNSCYTSATLKLWSLQGQKKLQEFLADMGMPLKQVKQKFNSMDISLKENLREMLEESANKFGMKDVRVQTFSVQFGFKNKFLASDIVFAVLSLLENTERDEKGTDNFIKALDSLSRSNLDKLHTGLEMGKKLLCAIQQTVASCICTNLILSQGPFLYCYLMEGTPDVKMFSNPISLCLLCKYLLKSFVCSTKNKRCKLLPLVLAAPLDAEKGTVIMVGIPPEAESSDKKNFFGRAFEKAAESTSSRTLHNHFDMSIIELRTEDRSKFLDALISLLS

Entity 11 polymer

描述 description	DNA replication complex GINS protein SLD5
分子量 formula_weight	25577.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	Q,K

MEDELALSDQGSDEDEEVLTPAELINKLEEAWLNEKFAPELLESKSEVVECVMEQLNHMEQNLHRAKPGDLKISFHHMEIERIRYMLSSYLRSRMLKIEKFFPHILEKEKSRGEGEPPHLSPEEFAFAKEYMTNTETLLKSVALRHMPPNLQTVDLLKSVPKPNLDSFVFLRVKEEQNNILVEPETDEQSEYAIDMEVGSQHLIRYRTIAPLVASGAVKLI

Entity 12 polymer

描述 description	Protein downstream neighbor of son homolog
分子量 formula_weight	63864.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	R,L

MAELLPGYSPSFKKPSEILRLSRRRSRSEASKTGLSPFSPGDVIKRVPGLRPFSPGPNKGAGVKRRNPFASLENTVCSPVKRRAETVAEYGAASLEPRALSAVRPSCLGQDSPEPPQFNSVEDVIWGDPLAADADPLVKTESPEKPAPACEIPKGSVTFPADWSLKTRLLFTSSHSFSWADHLKAQEEAQGLVMQCRATAVNLPHSIQEPKLSTDLRCAFQQSLVHWIHPSLPWVQLFPRIGVDRKMAGKNTPWSQDESLQQVLMSEWALSFTSLYNLLKAKLCPYFYVCTYQFTVLFRAAGLAGSDVITAVMSPTTRGLREAMKNEGITFSQPLVEDDTGKKQKKPEAASQGDINPEKENGTAEADEASDESDEDESFSWLEEMGVEDKIKKPDSISIKLRKEKNEVKLDHKPESVVLVKGTNTFTLLNFLINCKSIVAAAGLQAGLPPTLLSPVAFRGATMHALKARSVNVKTRVNSGYKDQFSLEITGPIMPHSLHSLTMLLQSAQRGSFSAGLYTHEPTAVFNTPIHSQAVKEISADLQNCGLHPCTVEQLTQVNELGKLSLRHLEMTDYRYTWK

Entity 13 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	triclinic

分辨率 resolution	3.14 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	100667

fit	/app/data/saxs_computation/q6/8q6o/8q6o.fit
pddf	/app/data/pr_computation/q6/8q6o/8q6o.pr.out
profile	/app/data/saxs_computation/q6/8q6o/8q6o.dat

X. laevis CMG dimer bound to dimeric DONSON - without ATPase

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (13)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

Entity 13 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)