SASDF39

Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Single concentration 最后更新:2020-02-12T18:29:36.378321+01:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1

浓度— – 3.0 缓冲液 / pH50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole / 8.0
实验温度35.0 设备 / 束线CEITEC / Rigaku BioSAXS-1000
波长0.154 nm曝光600.0 s × 6

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
ADP-ribosylation factor1 - short
查看序列
GGCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGCC
RNAHomo sapiens——–—monomer分子数 110.962 kDa
Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4
查看序列
GSHMKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK
proteinHomo sapiensO95793183–355monomer分子数 119.733 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
1198[3]0.016683–0.300425 1/A含误差列缺失 017sasbdb/entries/39/sasdf39/source/SASDF39.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)6.39—Å
i0Guinier0.190.00012arbitrary
i0P(r)0.1882—arbitrary
mwExperimental29.0—kDa
mwPorod24.3—kDa
porod_volumePorod39.0—ų
rgGuinier2.060.036Å
rgP(r)2.03—Å

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

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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50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole缓冲液浓度—
pH8.0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2018-05-29储存 / 测量温度20.0 / 35.0
曝光时间600.0帧数6
波长0.154样品-探测器距离0.48
光源X-ray in house探测器Pilatus 100K
机构 / 束线CEITEC / Rigaku BioSAXS-1000 · Brno, Czech Republic
q 范围0.167 – 3.004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
curvesasbdb/entries/39/sasdf39/source/SASDF39.datdownloaded624482df61ad75d87caede69e83aba8e2e08fa1ed3b5e3dabc34614500fcc1843a38下载查看原文件源站
full_entry_zipsasbdb/entries/39/sasdf39/source/SASDF39.zipdownloaded8662329e72f218cbd0cab3ebbcbdd5ff6183b38fb07c6abb7fb2ab78d939e35c01d664下载查看原文件源站
pddfsasbdb/entries/39/sasdf39/source/SASDF39.outdownloaded2250603c83460dd6c3ab4fd3a0e9530b69451e5ebed4849350962e56d1a61641c4fa2下载查看原文件源站
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summarysasbdb/entries/39/sasdf39/source/summary.jsondownloaded87887ef0058b085cd843e0bad67fffa550489dd144429bcda9660f3b0d033bee7346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(4 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:173 个字段值
字段路径原始值
codeSASDF39
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleStaufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.
project.publication.titleStaufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.
project.publication.author_listYadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gkz1163
project.publication.pmid31875226
project.publication.published_date2019 Dec 25
project.statusreleased
project.submitted_date2019-07-08
project.released_date2019-11-29
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDF39.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDF39.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF39_dat_img.png
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intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF39_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDF39.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 100K
experiment.instrument.detector.resolution172.0
experiment.instrument.nameCEITEC
experiment.instrument.cityBrno
experiment.instrument.countryCzech Republic
experiment.instrument.beamline_nameRigaku BioSAXS-1000
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray in house
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_nameADP-ribosylation factor1 - short
experiment.sample.molecule[0].short_nameARF1 RNA - short
experiment.sample.molecule[0].sequenceGGCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGCC
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeRNA
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw10.962
experiment.sample.molecule[0].total_mw10.962
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.molecule[1].long_nameDouble-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4
experiment.sample.molecule[1].short_nameSTAU1-RBD34
experiment.sample.molecule[1].sequenceGSHMKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKNAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKEKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFK
experiment.sample.molecule[1].organismHomo sapiens
experiment.sample.molecule[1].uniprot_codeO95793
experiment.sample.molecule[1].uniprot_range_first183
experiment.sample.molecule[1].uniprot_range_last355
experiment.sample.molecule[1].oligomerizationmonomer
experiment.sample.molecule[1].molecular_typeprotein
experiment.sample.molecule[1].uniprot_sequenceMSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS ITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF PVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN LNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN AAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE KEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ PTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM VPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH VPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES CHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC
experiment.sample.molecule[1].mw19.733
experiment.sample.molecule[1].total_mw19.733
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.buffer.name50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameDouble-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressnull
experiment.contributor[0].affiliation[0].full_nameCEITEC - Central European Institute of Technology, Masaryk University
experiment.contributor[0].affiliation[0].webpagehttps://www.ceitec.eu/
experiment.contributor[0].contributor_nameTomas
experiment.contributor[0].contributor_surnameKlumpler
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2018-05-29
experiment.storage_temperature20.0
experiment.cell_temperature35.0
experiment.exposure_time600.0
experiment.number_of_frames6
experiment.wavelength0.154
experiment.sample_detector_distance0.48
experiment.concentration_minnull
experiment.concentration_max3.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.167
experiment.s_max3.004
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDF39_fit1_model1_img.png
fits[0].models[0].softwareOther
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_versionnull
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fits[0].models[0].model_mw611.6
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user195
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value1.244
fits[0].p_value0.327758
fits[0].fit_residual_plotSASDF39_fit1_fitresiduals_img.png
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fits[0].software_version2.8.3
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1 in 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH 8 were collected using a Rigaku BioSAXS-1000 instrument (CEITEC; Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 35°C. Six successive 600 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.
tags[]
intensity_unitarbitrary
experimental_mw29.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw24.3
porod_mw_errornull
pddf_i00.1882
pddf_i0_errornull
guinier_i00.19
guinier_i0_error0.00012
pddf_rg2.03
pddf_rg_errornull
guinier_rg2.06
guinier_rg_error0.036
pddf_dmax6.39
pddf_dmax_errornull
porod_volume39.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last33
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDF39_datloglog_img.png
symmetrynull
last_modified2020-02-12T18:29:36.378321+01:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDF39
statussuccess
started_at2026-08-11T16:04:57.375156+00:00
finished_at2026-08-11T16:05:07.336855+00:00
source_last_modified2020-02-12T18:29:36.378321+01:00
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查看完整 summary.json 原文
{
  "code": "SASDF39",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.",
    "publication": {
      "title": "Staufen1 reads out structure and sequence features in ARF1 dsRNA for target recognition.",
      "author_list": "Yadav DK, Zigáčková D, Zlobina M, Klumpler T, Beaumont C, Kubíčková M, Vaňáčová Š, Lukavsky PJ",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkz1163",
      "pmid": "31875226",
      "published_date": "2019 Dec 25"
    },
    "status": "released",
    "submitted_date": "2019-07-08",
    "released_date": "2019-11-29"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDF39.dat",
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDF39_pofr_img.png",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDF39.sascif",
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        "type": null,
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      },
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      "city": "Brno",
      "country": "Czech Republic",
      "beamline_name": "Rigaku BioSAXS-1000",
      "beam_geometry": "",
      "type_of_source": "X-ray in house",
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      "xray_energy": null,
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      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "ADP-ribosylation factor1 - short",
          "short_name": "ARF1 RNA - short",
          "sequence": "GGCAGAAGCUGCCUCUUCGGAGGCAGUUUCUGCC",
          "organism": "Homo sapiens",
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          "molecular_type": "RNA",
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          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4",
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          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSQVQVQVQNPSAALSGSQILNKNQSLLSQPLMSIPSTTSSLPSENAGRPIQNSALPSAS\nITSTSAAAESITPTVELNALCMKLGKKPMYKPVDPYSRMQSTYNYNMRGGAYPPRYFYPF\nPVPPLLYQVELSVGGQQFNGKGKTRQAAKHDAAAKALRILQNEPLPERLEVNGRESEEEN\nLNKSEISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSKKISKKN\nAAIAVLEELKKLPPLPAVERVKPRIKKKTKPIVKPQTSPEYGQGINPISRLAQIQQAKKE\nKEPEYTLLTERGLPRRREFVMQVKVGNHTAEGTGTNKKVAKRNAAENMLEILGFKVPQAQ\nPTKPALKSEEKTPIKKPGDGRKVTFFEPGSGDENGTSNKEDEFRMPYLSHQQLPAGILPM\nVPEVAQAVGVSQGHHTKDFTRAAPNPAKATVTAMIARELLYGGTSPTAETILKNNISSGH\nVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKNNKNEFVSLINCSSQPPLISHGIGKDVES\nCHDMAALNILKLLSELDQQSTEMPRTGNGPMSVCGRC",
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          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": null,
            "full_name": "CEITEC - Central European Institute of Technology, Masaryk University",
            "webpage": "https://www.ceitec.eu/"
          }
        ],
        "contributor_name": "Tomas",
        "contributor_surname": "Klumpler",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2018-05-29",
    "storage_temperature": 20.0,
    "cell_temperature": 35.0,
    "exposure_time": 600.0,
    "number_of_frames": 6,
    "wavelength": 0.154,
    "sample_detector_distance": 0.48,
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  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF39_fit1_model1_img.png",
          "software": "Other",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF39_fit1_model1.pdb",
          "model_mw": 611.6,
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          "user": 195
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDF39_fit1_fixed_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 1.244,
      "p_value": 0.327758,
      "fit_residual_plot": "SASDF39_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF39_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/dsRBD34_hARF-for-deposition-2019-01-03-100.log",
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  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "SAXS data from solutions of double-stranded RNA-binding protein Staufen homolog 1 - RNA binding domain 3 and 4 - in complex with STAU1 binding site within the ADP-ribosylation factor1 in 50 mM sodium phosphate buffer, 300 mM NaCl, 500 mM imidazole, pH 8 were collected using a Rigaku BioSAXS-1000 instrument (CEITEC; Brno, Czech Republic) equipped with a Pilatus 100K detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.00 mg/ml was measured at 35°C. Six successive 600 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.",
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  "experimental_mw_error": null,
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  "estimated_volume": null,
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  "pddf_point_first": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDF39_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2020-02-12T18:29:36.378321+01:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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