SASDEP4

Protein tyrosine phosphatase SHP2 with E76K activating mutation

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Merged 最后更新:2019-12-06T13:07:15.624532+01:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Protein tyrosine phosphatase SHP2 with E76K activating mutation

浓度0.76 – 12.2 缓冲液 / pH50 mM ADA, 2 mM TCEP / 6.5
实验温度20.0 设备 / 束线Stanford Synchrotron Radiation Lightsource (SSRL) / BL4-2
波长0.1127 nm曝光1.0 s × 10

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Tyrosine-protein phosphatase non-receptor type 11 E76K
查看序列
GSGMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAKLVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRI
proteinHomo sapiensQ061241–529monomer分子数 160.911 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
1365[3]0.0140536–0.350002 1/A含误差列缺失 00sasbdb/entries/p4/sasdep4/source/SASDEP4.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)9.53—Å
i0Guinier142.70.44arbitrary
i0P(r)143.3—arbitrary
mwExperimental53.15—kDa
rgGuinier2.910.062Å
rgP(r)2.95—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 ADA, 2 mM TCEP缓冲液浓度—
pH6.5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2016-03-28储存 / 测量温度4.0 / 20.0
曝光时间1.0帧数10
波长0.1127样品-探测器距离1.65
光源X-ray synchrotron探测器Rayonix MX225-HE
机构 / 束线Stanford Synchrotron Radiation Lightsource (SSRL) / BL4-2 · Menlo Park, CA, USA
q 范围0.141 – 3.5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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full_entry_zipsasbdb/entries/p4/sasdep4/source/SASDEP4.zipdownloaded102529d0db7b8e4bad8ee60d122b3fdc3180eb478b415b732d317a3d19cd8fba303cd5下载查看原文件源站
pddfsasbdb/entries/p4/sasdep4/source/SASDEP4.outdownloaded30072f19f6788203a9f05ac7c665caa05ffeb5e64eb78823718d64fbf348a54069d43下载查看原文件源站
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summarysasbdb/entries/p4/sasdep4/source/summary.jsondownloaded8591f9d1645d43cff1d11110c9467031c3b290b69f30d4ddc9213ee9b6b758aef387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:159 个字段值
字段路径原始值
codeSASDEP4
statusPublished
type_of_curveMerged
angular_unit1/A
project.titleMechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.
project.publication.titleMechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.
project.publication.author_listPádua RAP, Sun Y, Marko I, Pitsawong W, Stiller JB, Otten R, Kern D
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-018-06814-w
project.publication.pmid30375376
project.publication.published_date2018 Oct 30
project.statusreleased
project.submitted_date2018-09-14
project.released_date2018-11-05
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDEP4.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDEP4.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEP4_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDEP4.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.nameRayonix MX225-HE
experiment.instrument.detector.resolutionnull
experiment.instrument.nameStanford Synchrotron Radiation Lightsource (SSRL)
experiment.instrument.cityMenlo Park, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_nameBL4-2
experiment.instrument.beam_geometrynull
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_nameTyrosine-protein phosphatase non-receptor type 11 E76K
experiment.sample.molecule[0].short_nameSHP2 E76K
experiment.sample.molecule[0].sequenceGSGMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG DYYDLYGGEKFATLAKLVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGK EAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYD VGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETT DKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEP VSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV ERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHF RTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIR EKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRI
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ06124
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last529
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG DYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGK EAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYD VGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETT DKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEP VSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV ERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHF RTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIR EKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGH EYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARVYENVGLMQQQKSFR
experiment.sample.molecule[0].mw60.911
experiment.sample.molecule[0].total_mw60.911
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.buffer.name50 mM ADA, 2 mM TCEP
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameProtein tyrosine phosphatase SHP2 with E76K activating mutation
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].addressChevy Chase, USA
experiment.contributor[0].affiliation[0].full_nameHoward Hughes Medical Institute, Department of Biochemistry, Brandeis University
experiment.contributor[0].affiliation[0].webpagehttps://www.hhmi.org/
experiment.contributor[0].contributor_nameRIcardo
experiment.contributor[0].contributor_surnamePadua
experiment.contributor[0].orcidhttps://orcid.org/0000-0001-9719-3440
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-03-28
experiment.storage_temperature4.0
experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames10
experiment.wavelength0.1127
experiment.sample_detector_distance1.65
experiment.concentration_min0.76
experiment.concentration_max12.2
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.141
experiment.s_max3.5
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDEP4_fit1_model1_img.png
fits[0].models[0].softwareAllosMod
fits[0].models[0].pdb_link[0].pdb_code6cmq
fits[0].models[0].pdb_link[0].ext_code6CMQ
fits[0].models[0].pdb_link[0].ext_typepdb
fits[0].models[0].pdb_link[0].difference_with_modelderived
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_versionnull
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDEP4_fit1_model1.pdb
fits[0].models[0].model_mw60.91
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].user367
fits[0].fit_unit1/A
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fits[0].softwareMultiFoXS
fits[0].chi_square_value2.535761
fits[0].p_value0.0
fits[0].fit_residual_plotmulti_state_model_88pdb_fitfoxsresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDEP4_fit1.dat
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Protein tyrosine phosphatase SHP2 with E76K activating mutation in 50 mM ADA, 2 mM TCEP, pH 6.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Stanford, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.8 and 12.2 mg/ml were measured at 20°C. 10 successive 1 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.
tags[]
intensity_unitarbitrary
experimental_mw53.15
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i0143.3
pddf_i0_errornull
guinier_i0142.7
guinier_i0_error0.44
pddf_rg2.95
pddf_rg_errornull
guinier_rg2.91
guinier_rg_error0.062
pddf_dmax9.53
pddf_dmax_errornull
porod_volumenull
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last34
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEP4_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDEP4
statussuccess
started_at2026-08-11T14:28:02.047392+00:00
finished_at2026-08-11T14:28:10.544630+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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查看完整 summary.json 原文
{
  "code": "SASDEP4",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.",
    "publication": {
      "title": "Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2.",
      "author_list": "Pádua RAP, Sun Y, Marko I, Pitsawong W, Stiller JB, Otten R, Kern D",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-018-06814-w",
      "pmid": "30375376",
      "published_date": "2018 Oct 30"
    },
    "status": "released",
    "submitted_date": "2018-09-14",
    "released_date": "2018-11-05"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEP4.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEP4.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEP4_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP4_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEP4.sascif",
  "experiment": {
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        "resolution": null
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    },
    "sample": {
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        {
          "long_name": "Tyrosine-protein phosphatase non-receptor type 11 E76K",
          "short_name": "SHP2 E76K",
          "sequence": "GSGMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG\r\nDYYDLYGGEKFATLAKLVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGK\r\nEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYD\r\nVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETT\r\nDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEP\r\nVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV\r\nERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHF\r\nRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIR\r\nEKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRI",
          "organism": "Homo sapiens",
          "uniprot_code": "Q06124",
          "uniprot_range_first": 1,
          "uniprot_range_last": 529,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTG\nDYYDLYGGEKFATLAELVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGK\nEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYD\nVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETT\nDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEP\nVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEV\nERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHF\nRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIR\nEKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKSKRKGH\nEYTNIKYSLADQTSGDQSPLPPCTPTPPCAEMREDSARVYENVGLMQQQKSFR",
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          "total_mw": 60.911,
          "number_molecules": 1,
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          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "50 mM ADA, 2 mM TCEP",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 6.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Protein tyrosine phosphatase SHP2 with E76K activating mutation",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Chevy Chase, USA",
            "full_name": "Howard Hughes Medical Institute, Department of Biochemistry, Brandeis University",
            "webpage": "https://www.hhmi.org/"
          }
        ],
        "contributor_name": "RIcardo",
        "contributor_surname": "Padua",
        "orcid": "https://orcid.org/0000-0001-9719-3440"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-03-28",
    "storage_temperature": 4.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 10,
    "wavelength": 0.1127,
    "sample_detector_distance": 1.65,
    "concentration_min": 0.76,
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    "s_min": 0.141,
    "s_max": 3.5,
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP4_fit1_model1_img.png",
          "software": "AllosMod",
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              "ext_code": "6CMQ",
              "ext_type": "pdb",
              "difference_with_model": "derived"
            }
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          "bead_radius": null,
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          "user": 367
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/multi_state_model_88pdb_fitfoxs_img.png",
      "software": "MultiFoXS",
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      "fit_residual_plot": "multi_state_model_88pdb_fitfoxsresiduals_img.png",
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  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Protein tyrosine phosphatase SHP2 with E76K activating mutation in 50 mM ADA, 2 mM TCEP, pH 6.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL; Stanford, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.1127 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.8 and 12.2 mg/ml were measured at 20°C. 10 successive 1 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
  "tags": [],
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDEP4_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
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}
查看完整 manifest.json 原文
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