SASDCW6

Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2021-08-18T17:30:42.937574+02:00

12N12 nucleosomes in the presence of the chromatin remodeler Chd1 in 60% sucrose and AMP-PNP. The complex formed contains two Chd1 proteins bound to each nucleosome. Due to contrast matching between the solvent and histone proteins, the measured signal is dominated by the DNA component. The models were generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the following model key/list that sequentially corresponds to models displayed in this entry ordered from top-to-bottom: -------------------------------------------------------------------------------------------------------- --------------SASDCW6_fit1_model1=Chd1_12N12_AMP_01_wrapped_25perc; --------------SASDCW6_fit1_model2=Chd1_12N12_AMP_02_wrapped_01perc; --------------SASDCW6_fit1_model3=Chd1_12N12_AMP_03_wrapped_01perc; --------------SASDCW6_fit1_model4=Chd1_12N12_AMP_04_extreme_02perc; --------------SASDCW6_fit1_model5=Chd1_12N12_AMP_05_extreme_01perc; --------------SASDCW6_fit1_model6=Chd1_12N12_AMP_06_inplane_01perc; --------------SASDCW6_fit1_model7=Chd1_12N12_AMP_07_inplane_11perc; --------------SASDCW6_fit1_model8=Chd1_12N12_AMP_08_inplane_08perc; --------------SASDCW6_fit1_model9=Chd1_12N12_AMP_09_inplane_03perc; --------------SASDCW6_fit1_model10=Chd1_12N12_AMP_10_inplane_12perc; --------------SASDCW6_fit1_model11=Chd1_12N12_AMP_11_inplane_01perc; --------------SASDCW6_fit1_model12=Chd1_12N12_AMP_12_inplane_03perc_dyadfliip; --------------SASDCW6_fit1_model13=Chd1_12N12_AMP_13_inplane_12perc_dyadflip; --------------SASDCW6_fit1_model14=Chd1_12N12_AMP_14_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model15=Chd1_12N12_AMP_15_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model16=Chd1_12N12_AMP_16_inplane_15perc; --------------SASDCW6_fit1_model17=Chd1_12N12_AMP_17_inplane_02perc.

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Chd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP

浓度— – 1.88 缓冲液 / pH10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP / 7.8
实验温度25.0 设备 / 束线Cornell High Energy Synchrotron Source (CHESS) / G1
波长0.1109 nm曝光10.0 s × 40

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Chromodomain-helicase-DNA-binding protein 1
查看序列
GPQSTVKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGIDIVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLKRLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRFEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILEYAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAEDHVTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQLEMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYKAILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEKHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDLKYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRDDPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYLLSFLRGGLNTKSPS
proteinSaccharomyces cerevisiaeP32657118–1274dimer分子数 2133.115 kDa
169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)
查看序列
CTTTCAGCTGATATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATCTTGATATCAGCTGAAAG
DNA———–—monomer分子数 152.468 kDa
Histone H2A type 1
查看序列
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKKTESAKSAKSK
proteinXenopus laevisP06897—–—monomer分子数 113.966 kDa
Histone H2B 1.1
查看序列
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
proteinXenopus laevisP02281—–—monomer分子数 113.934 kDa
Histone H3.2
查看序列
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
proteinXenopus laevisP842331–136monomer分子数 115.388 kDa
Histone H4
查看序列
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
proteinXenopus laevisP62799—–—monomer分子数 111.367 kDa

实验曲线

曲线点数 / 列q 范围误差质量负强度点来源文件
1245[3]0.016–0.26 1/A含误差列缺失 022sasbdb/entries/w6/sasdcw6/source/SASDCW6.dat
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2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
dmaxP(r)16.7—Å
i0Guinier0.02160.00037arbitrary
i0P(r)0.021220.00017arbitrary
mwExperimental105.0—kDa
rgGuinier5.6190.119Å
rgP(r)5.5270.049Å

这些数值是 SASBDB 来源记录,不是 SAXSdb 对实验曲线重新计算的结果。

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3. 来源拟合与模型 Source Fits & Models

拟合 1 · EOM/GAJOE

χ²:0.87CorMap p:0.6841单位:1/A
模型名称 / 类型软件对称性模型 MWPDB 声明来源文件
1—atomicCustom in-house —100.1—模型 图片
2—atomicCustom in-house —100.1—模型 图片
3—atomicCustom in-house —100.1—模型 图片
4—atomicCustom in-house —100.1—模型 图片
5—atomicCustom in-house —100.1—模型 图片
6—atomicCustom in-house —100.1—模型 图片
7—atomicCustom in-house —100.1—模型 图片
8—atomicCustom in-house —100.1—模型 图片
9—atomicCustom in-house —100.1—模型 图片
10—atomicCustom in-house —100.1—模型 图片
11—atomicCustom in-house —100.1—模型 图片
12—atomicCustom in-house —100.1—模型 图片
13—atomicCustom in-house —100.1—模型 图片
14—atomicCustom in-house —100.1—模型 图片
15—atomicCustom in-house —100.1—模型 图片
16—atomicCustom in-house —100.1—模型 图片
17—atomicCustom in-house —100.1—模型 图片
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4. 来源文件索引 Source Files

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5. 实验说明与论文 Experiment & Publication

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6. 完整来源记录 Complete Source Record

下列内容直接来自 SASBDB 条目。字段没有值时显示“—”;未声明的单位不会由 SAXSdb 猜测。

打开 SASBDB 原始条目

缓冲液与样品属性

缓冲液名称10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP缓冲液浓度—
pH7.8添加剂—
缓冲液说明—
纯度测定方法—消光系数—
吸收值—散射对比度—
比体积 / 干体积— / —混合物 / 氘代— / —

采集条件与仪器

测量日期2015-10-24储存 / 测量温度25.0 / 25.0
曝光时间10.0帧数40
波长0.1109样品-探测器距离2.08
光源X-ray synchrotron探测器Pilatus 200K
机构 / 束线Cornell High Energy Synchrotron Source (CHESS) / G1 · Ithaca, NY, USA
q 范围0.16 – 2.6样品体积 / 流速— / —

SASBDB 原始图

实验 I(q)
实验 I(q)
实验 I(q) log-log
实验 I(q) log-log
Guinier 图
Guinier 图
Kratky 图
Kratky 图
P(r) 图
P(r) 图

可下载文件

类别文件状态大小校验值下载与查看
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summarysasbdb/entries/w6/sasdcw6/source/summary.jsondownloaded2653858308419875f7c50d6c8d6a77eafe2919cc6fc010582693e58c75e9b1fdf4584下载查看原文件源站
curve:来源记录
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full_entry_zip:来源记录与 ZIP 内部目录(21 项)
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pddf:来源记录
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sascif:来源记录
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summary:来源记录
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全部来源字段(无筛选)

这里自动展开来源记录中的每一个字段,包括空值、列表成员和页面上方已展示过的字段。

summary.json:449 个字段值
字段路径原始值
codeSASDCW6
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleThe ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome.
project.publication.titleThe ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome.
project.publication.author_listTokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gky206
project.publication.pmid29850894
project.publication.published_date2018 Jun 1
project.statusreleased
project.submitted_date2017-08-03
project.released_date2018-03-25
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDCW6.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDCW6.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCW6_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCW6_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCW6_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCW6_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDCW6.sascif
experiment.instrument.detector.typePilatus
experiment.instrument.detector.namePilatus 200K
experiment.instrument.detector.resolution172.0
experiment.instrument.nameCornell High Energy Synchrotron Source (CHESS)
experiment.instrument.cityIthaca, NY
experiment.instrument.countryUSA
experiment.instrument.beamline_nameG1
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
experiment.instrument.line_collimation_slitlengthnull
experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_nameChromodomain-helicase-DNA-binding protein 1
experiment.sample.molecule[0].short_nameChd1
experiment.sample.molecule[0].sequenceGPQSTVKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVH EASANPQPEDFHGIDIVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLI KWTDESHLHNTWETYESIGQVRGLKRLDNYCKQFIIEDQQVRLDPYVTAE DIEIMDMERERRLDEFEEFHVPERIIDSQRASLEDGTSQLQYLVKWRRLN YDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPRFEKLS VQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFI SWLIFARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDT IREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEA HRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFLMPGRFT IDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILR VELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASNHPYLF DNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVL IFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDF VFLLSTRAGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVM VYRLVSKDTVEEEVLERARKKMILEYAIISLGVTDGNKYTKKNEPNAGEL SAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAEDHVTTPDLGESHLGGE EFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQLEMMN RRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEV RALYKAILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVH EEEKNRKEILEKLEKHATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREK KAVLFNFKGVKSLNAESLLSRVEDLKYLKNLINSNYKDDPLKFSLGNNTP KPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRDDPFLGITDKIFLNEV HNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYLLSFLR GGLNTKSPS
experiment.sample.molecule[0].organismSaccharomyces cerevisiae
experiment.sample.molecule[0].uniprot_codeP32657
experiment.sample.molecule[0].uniprot_range_first118
experiment.sample.molecule[0].uniprot_range_last1274
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMAAKDISTEVLQNPELYGLRRSHRAAAHQQNYFNDSDDEDDEDNIKQSRRKRMTTIEDDE DEFEDEEGEEDSGEDEDEEDFEEDDDYYGSPIKQNRSKPKSRTKSKSKSKPKSQSEKQST VKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGID IVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLK RLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLED GTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPR FEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIF ARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGK KTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLI TGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKK DVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASN HPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQM VRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINL MTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILE YAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAED HVTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQ LEMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYK AILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEK HATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDL KYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRD DPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYL LSFLRGGLNTKSPSADIGSKKLPTGPSKKRQRKPANHSKSMTPEITSSEPANGPPSKRMK ALPKGPAALINNTRLSPNSPTPPLKSKVSRDNGTRQSSNPSSGSAHEKEYDSMDEEDCRH TMSAIRTSLKRLRRGGKSLDRKEWAKILKTELTTIGNHIESQKGSSRKASPEKYRKHLWS YSANFWPADVKSTKLMAMYDKITESQKK
experiment.sample.molecule[0].mw133.115
experiment.sample.molecule[0].total_mw266.23
experiment.sample.molecule[0].number_molecules2
experiment.sample.molecule[0].complex_stateTrue
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.molecule[1].long_name169 bp DNA (145 bp Widom 601, flanked by 12bp DNA)
experiment.sample.molecule[1].short_nameDNA
experiment.sample.molecule[1].sequenceCTTTCAGCTGATATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATCTTGATATCAGCTGAAAG
experiment.sample.molecule[1].organismnull
experiment.sample.molecule[1].uniprot_codenull
experiment.sample.molecule[1].uniprot_range_firstnull
experiment.sample.molecule[1].uniprot_range_lastnull
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeDNA
experiment.sample.molecule[1].uniprot_sequencenull
experiment.sample.molecule[1].mw52.468
experiment.sample.molecule[1].total_mw52.468
experiment.sample.molecule[1].number_molecules1
experiment.sample.molecule[1].complex_stateFalse
experiment.sample.molecule[1].deuterationnull
experiment.sample.molecule[1].molecule_sourcebiological
experiment.sample.molecule[1].molecule_descriptionnull
experiment.sample.molecule[2].long_nameHistone H2A type 1
experiment.sample.molecule[2].short_nameH2A
experiment.sample.molecule[2].sequenceMSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK TESAKSAKSK
experiment.sample.molecule[2].organismXenopus laevis
experiment.sample.molecule[2].uniprot_codeP06897
experiment.sample.molecule[2].uniprot_range_firstnull
experiment.sample.molecule[2].uniprot_range_lastnull
experiment.sample.molecule[2].oligomerizationmonomer
experiment.sample.molecule[2].molecular_typeprotein
experiment.sample.molecule[2].uniprot_sequenceMSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK TESAKSAKSK
experiment.sample.molecule[2].mw13.966
experiment.sample.molecule[2].total_mw13.966
experiment.sample.molecule[2].number_molecules1
experiment.sample.molecule[2].complex_stateFalse
experiment.sample.molecule[2].deuterationnull
experiment.sample.molecule[2].molecule_sourcebiological
experiment.sample.molecule[2].molecule_descriptionnull
experiment.sample.molecule[3].long_nameHistone H2B 1.1
experiment.sample.molecule[3].short_nameH2B
experiment.sample.molecule[3].sequenceMPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT KYTSAK
experiment.sample.molecule[3].organismXenopus laevis
experiment.sample.molecule[3].uniprot_codeP02281
experiment.sample.molecule[3].uniprot_range_firstnull
experiment.sample.molecule[3].uniprot_range_lastnull
experiment.sample.molecule[3].oligomerizationmonomer
experiment.sample.molecule[3].molecular_typeprotein
experiment.sample.molecule[3].uniprot_sequenceMPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAM SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT KYTSAK
experiment.sample.molecule[3].mw13.934
experiment.sample.molecule[3].total_mw13.934
experiment.sample.molecule[3].number_molecules1
experiment.sample.molecule[3].complex_stateFalse
experiment.sample.molecule[3].deuterationnull
experiment.sample.molecule[3].molecule_sourcebiological
experiment.sample.molecule[3].molecule_descriptionnull
experiment.sample.molecule[4].long_nameHistone H3.2
experiment.sample.molecule[4].short_nameH3
experiment.sample.molecule[4].sequenceMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI MPKDIQLARRIRGERA
experiment.sample.molecule[4].organismXenopus laevis
experiment.sample.molecule[4].uniprot_codeP84233
experiment.sample.molecule[4].uniprot_range_first1
experiment.sample.molecule[4].uniprot_range_last136
experiment.sample.molecule[4].oligomerizationmonomer
experiment.sample.molecule[4].molecular_typeprotein
experiment.sample.molecule[4].uniprot_sequenceMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI MPKDIQLARRIRGERA
experiment.sample.molecule[4].mw15.388
experiment.sample.molecule[4].total_mw15.388
experiment.sample.molecule[4].number_molecules1
experiment.sample.molecule[4].complex_stateFalse
experiment.sample.molecule[4].deuterationnull
experiment.sample.molecule[4].molecule_sourcebiological
experiment.sample.molecule[4].molecule_descriptionnull
experiment.sample.molecule[5].long_nameHistone H4
experiment.sample.molecule[5].short_nameH4
experiment.sample.molecule[5].sequenceMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
experiment.sample.molecule[5].organismXenopus laevis
experiment.sample.molecule[5].uniprot_codeP62799
experiment.sample.molecule[5].uniprot_range_firstnull
experiment.sample.molecule[5].uniprot_range_lastnull
experiment.sample.molecule[5].oligomerizationmonomer
experiment.sample.molecule[5].molecular_typeprotein
experiment.sample.molecule[5].uniprot_sequenceMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
experiment.sample.molecule[5].mw11.367
experiment.sample.molecule[5].total_mw11.367
experiment.sample.molecule[5].number_molecules1
experiment.sample.molecule[5].complex_stateFalse
experiment.sample.molecule[5].deuterationnull
experiment.sample.molecule[5].molecule_sourcebiological
experiment.sample.molecule[5].molecule_descriptionnull
experiment.sample.buffer.name10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.8
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameChd1-12N12, chromatin remodeler--nucleosome complex, in 60% sucrose with AMP-PNP
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
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experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressIthaca, NY, United States
experiment.contributor[0].affiliation[0].full_nameCornell University
experiment.contributor[0].affiliation[0].webpagehttps://www.cornell.edu/
experiment.contributor[0].contributor_nameJoshua
experiment.contributor[0].contributor_surnameTokuda
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-10-24
experiment.storage_temperature25.0
experiment.cell_temperature25.0
experiment.exposure_time10.0
experiment.number_of_frames40
experiment.wavelength0.1109
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experiment.sample_volumenull
experiment.flow_ratenull
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experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[16].software_versionnull
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fits[0].models[16].model_mw100.1
fits[0].models[16].bead_radius1.9
fits[0].models[16].lognull
fits[0].models[16].symmetrynull
fits[0].models[16].commentGenerated using 3D-DART and custom scripts written in Pymol. Percentage represents ensemble weight.
fits[0].models[16].user170
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCW6_fit1_fixed_fit_img.png
fits[0].softwareEOM/GAJOE
fits[0].chi_square_value0.87
fits[0].p_value0.6841
fits[0].fit_residual_plotfit4columns1049_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDCW6_fit1.fit
fits[0].fit_lognull
fits[0].software_version
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionVersion 5.0 (r4547)
i0_calibration_standardnull
description12N12 nucleosomes in the presence of the chromatin remodeler Chd1 in 60% sucrose and AMP-PNP. The complex formed contains two Chd1 proteins bound to each nucleosome. Due to contrast matching between the solvent and histone proteins, the measured signal is dominated by the DNA component. The models were generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the following model key/list that sequentially corresponds to models displayed in this entry ordered from top-to-bottom: -------------------------------------------------------------------------------------------------------- --------------SASDCW6_fit1_model1=Chd1_12N12_AMP_01_wrapped_25perc; --------------SASDCW6_fit1_model2=Chd1_12N12_AMP_02_wrapped_01perc; --------------SASDCW6_fit1_model3=Chd1_12N12_AMP_03_wrapped_01perc; --------------SASDCW6_fit1_model4=Chd1_12N12_AMP_04_extreme_02perc; --------------SASDCW6_fit1_model5=Chd1_12N12_AMP_05_extreme_01perc; --------------SASDCW6_fit1_model6=Chd1_12N12_AMP_06_inplane_01perc; --------------SASDCW6_fit1_model7=Chd1_12N12_AMP_07_inplane_11perc; --------------SASDCW6_fit1_model8=Chd1_12N12_AMP_08_inplane_08perc; --------------SASDCW6_fit1_model9=Chd1_12N12_AMP_09_inplane_03perc; --------------SASDCW6_fit1_model10=Chd1_12N12_AMP_10_inplane_12perc; --------------SASDCW6_fit1_model11=Chd1_12N12_AMP_11_inplane_01perc; --------------SASDCW6_fit1_model12=Chd1_12N12_AMP_12_inplane_03perc_dyadfliip; --------------SASDCW6_fit1_model13=Chd1_12N12_AMP_13_inplane_12perc_dyadflip; --------------SASDCW6_fit1_model14=Chd1_12N12_AMP_14_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model15=Chd1_12N12_AMP_15_inplane_01perc_dyadflip; --------------SASDCW6_fit1_model16=Chd1_12N12_AMP_16_inplane_15perc; --------------SASDCW6_fit1_model17=Chd1_12N12_AMP_17_inplane_02perc.
experiment_descriptionSynchrotron SAXS data from solutions of Chd1-12N12, chromatin remodeler--nucleosome complex, in 10 mM Tris, 100 mM NaCl, 2 mM MgCl2, 0.1 mM EDTA, 1 mM DTT, 60% (w/v) sucrose, 0.5 mM AMP-PNP, pH 7.8, were collected on the G1 beam line at the Cornell High Energy Synchrotron Source (Ithaca, NY, USA) using a Pilatus Pilatus 200K detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1109 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 1.88 mg/ml was measured at 25°C. 40 successive 10 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted to produce the scattering profile displayed in this entry.
tags[]
intensity_unitarbitrary
experimental_mw105.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
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pddf_i0_error0.00017
guinier_i00.0216
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pddf_rg5.527
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pddf_dmax16.7
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guinier_point_first1
guinier_point_last8
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCW6_datloglog_img.png
symmetrynull
last_modified2021-08-18T17:30:42.937574+02:00
bragg_peak[]
manifest.json:36 个字段值
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codeSASDCW6
statussuccess
started_at2026-08-11T15:17:09.443374+00:00
finished_at2026-08-11T15:17:20.800624+00:00
source_last_modified2021-08-18T17:30:42.937574+02:00
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查看完整 summary.json 原文
{
  "code": "SASDCW6",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome.",
    "publication": {
      "title": "The ATPase motor of the Chd1 chromatin remodeler stimulates DNA unwrapping from the nucleosome.",
      "author_list": "Tokuda JM, Ren R, Levendosky RF, Tay RJ, Yan M, Pollack L, Bowman GD",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gky206",
      "pmid": "29850894",
      "published_date": "2018 Jun 1"
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  "description": "12N12 nucleosomes in the presence of the chromatin remodeler Chd1 in 60% sucrose and AMP-PNP.\r\nThe complex formed contains two Chd1 proteins bound to each nucleosome. Due to contrast matching between the solvent and histone proteins, the measured signal is dominated by the DNA component. The models were generated using 3D-DART and custom scripts written in Pymol. The percentage-weighting of each model in the ensemble ('XXXperc') is noted in the following model key/list that sequentially corresponds to models displayed in this entry ordered from top-to-bottom: --------------------------------------------------------------------------------------------------------\r\n--------------SASDCW6_fit1_model1=Chd1_12N12_AMP_01_wrapped_25perc;  \r\n--------------SASDCW6_fit1_model2=Chd1_12N12_AMP_02_wrapped_01perc;  \r\n--------------SASDCW6_fit1_model3=Chd1_12N12_AMP_03_wrapped_01perc;  \r\n--------------SASDCW6_fit1_model4=Chd1_12N12_AMP_04_extreme_02perc;  \r\n--------------SASDCW6_fit1_model5=Chd1_12N12_AMP_05_extreme_01perc;  \r\n--------------SASDCW6_fit1_model6=Chd1_12N12_AMP_06_inplane_01perc;  \r\n--------------SASDCW6_fit1_model7=Chd1_12N12_AMP_07_inplane_11perc;  \r\n--------------SASDCW6_fit1_model8=Chd1_12N12_AMP_08_inplane_08perc;  \r\n--------------SASDCW6_fit1_model9=Chd1_12N12_AMP_09_inplane_03perc;  \r\n--------------SASDCW6_fit1_model10=Chd1_12N12_AMP_10_inplane_12perc;  \r\n--------------SASDCW6_fit1_model11=Chd1_12N12_AMP_11_inplane_01perc;  \r\n--------------SASDCW6_fit1_model12=Chd1_12N12_AMP_12_inplane_03perc_dyadfliip;  \r\n--------------SASDCW6_fit1_model13=Chd1_12N12_AMP_13_inplane_12perc_dyadflip;  \r\n--------------SASDCW6_fit1_model14=Chd1_12N12_AMP_14_inplane_01perc_dyadflip;  \r\n--------------SASDCW6_fit1_model15=Chd1_12N12_AMP_15_inplane_01perc_dyadflip;  \r\n--------------SASDCW6_fit1_model16=Chd1_12N12_AMP_16_inplane_15perc;  \r\n--------------SASDCW6_fit1_model17=Chd1_12N12_AMP_17_inplane_02perc.",
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  "guinier_point_last": 8,
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  "last_modified": "2021-08-18T17:30:42.937574+02:00",
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}
查看完整 manifest.json 原文
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