SASDF92

Urokinase plasminogen activator surface receptor, uPAR, T51C-V70C

数据类型:SASBDB 实验数据 状态:Published 曲线类型:Merged 最后更新:2023-06-21T07:56:39.492710+02:00

Introduced disulfide in the first LU domain, DI, of uPAR (T51C-V70C).

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Urokinase plasminogen activator surface receptor, uPAR, T51C-V70C

浓度0.3 – 2.8 缓冲液 / pH20 mM PBS, 5 %(v/v) glycerol / 7.4
实验温度10.0 设备 / 束线PETRA III / EMBL P12
波长0.124 nm曝光0.05 s × 20

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Urokinase plasminogen activator surface receptor
查看序列
>SP|Q03405|UPAR_HUMANUROKINASEPLASMINOGENACTIVATORSURFACERECEPTOROS=HOMOSAPIENSGN=PLAURPE=1SV=1MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEELELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISCGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNGFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGPMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDVQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT
proteinHomo sapiensQ03405—–—monomer分子数 136.98 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
11814[3]0.072479–5.08791 1/nm含误差列缺失 028sasbdb/entries/92/sasdf92/source/SASDF92.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)8.90.5nm
i0Guinier0.0360.0011/cm
i0P(r)0.036080.0041/cm
mwExperimental46.108—kDa
mwGuinier I(0)46.1085.0kDa
mwPorod32.0—kDa
porod_volumePorod54.5—nm³
rgGuinier2.520.01nm
rgP(r)2.5920.02nm

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20 mM PBS, 5 %(v/v) glycerol缓冲液浓度—
pH7.4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2017-12-01储存 / 测量温度10.0 / 10.0
曝光时间0.05帧数20
波长0.124样品-探测器距离3.1
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.072 – 5.088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/92/sasdf92/source/SASDF92.datdownloaded81954b1d175a0651f1410a73083ac9341e3bc8dbb1c81b160ae546799fa65ad5f9db7下载查看原文件源站
full_entry_zipsasbdb/entries/92/sasdf92/source/SASDF92.zipdownloaded74125ca4387c0f312f76606b9e08ed09a43a3ed5b834e65fd4505135fcb366d715ab8下载查看原文件源站
pddfsasbdb/entries/92/sasdf92/source/SASDF92.outdownloaded994448f014290d0d3a3497540a392304ce3be7ebd62d0497d3c6cdd3f9b140910be1e下载查看原文件源站
sascifsasbdb/entries/92/sasdf92/source/SASDF92.sascifdownloaded298538168db16392fc2eeefe6fe438a9e74c54ffe943ed8f067bf1003028a062f9a7fa下载查看原文件源站
summarysasbdb/entries/92/sasdf92/source/summary.jsondownloaded82732d0b5aac8b7bce24a1ef59ede244345d59d6f539b4a20120dfa13227c3980240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:156 个字段值
字段路径原始值
codeSASDF92
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleDid evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?
project.publication.titleDid evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?
project.publication.author_listLeth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M
project.publication.journalJ Biol Chem
project.publication.doi10.1074/jbc.RA119.007847
project.publication.pmid30894413
project.publication.published_date2019 Mar 20
project.statusreleased
project.submitted_date2019-01-30
project.released_date2019-03-20
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDF92.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDF92.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF92_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDF92_kratky_img.png
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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDF92.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
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_nameUrokinase plasminogen activator surface receptor
experiment.sample.molecule[0].short_nameuPAR
experiment.sample.molecule[0].sequence>sp|Q03405|UPAR_HUMAN Urokinase plasminogen activator surface receptor OS=Homo sapiens GN=PLAUR PE=1 SV=1 MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL ELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC GSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG FHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP MNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV QYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ03405
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL ELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC GSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG FHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP MNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV QYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT
experiment.sample.molecule[0].mw36.98
experiment.sample.molecule[0].total_mw36.98
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_statenull
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name20 mM PBS, 5 %(v/v) glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.4
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameUrokinase plasminogen activator surface receptor, uPAR, T51C-V70C
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_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameHaydyn
experiment.contributor[0].contributor_surnameMertens
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-12-01
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time0.05
experiment.number_of_frames20
experiment.wavelength0.124
experiment.sample_detector_distance3.1
experiment.concentration_min0.3
experiment.concentration_max2.8
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.072
experiment.s_max5.088
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDF92_fit1_model1_img.png
fits[0].models[0].softwareDAMMIN
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_versionnull
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fits[0].models[0].model_mw31.531
fits[0].models[0].bead_radius2.5
fits[0].models[0].loghttps://www.sasbdb.org/media/log_files/ref_rrm3HMB.log
fits[0].models[0].symmetrynull
fits[0].models[0].commentRefined DAMMIN model from average volume (10 DAMMIF iterations)
fits[0].models[0].user12
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/ref_ibuMksD_fit_img.png
fits[0].softwareDAMMIN
fits[0].chi_square_value0.955
fits[0].p_value0.89146
fits[0].fit_residual_plotref_ibuMksD_fitresiduals_img.png
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fits[0].software_version5.3
fits[0].descriptionRefined DAMMIN model from average volume (10 DAMMIF iterations)
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionIntroduced disulfide in the first LU domain, DI, of uPAR (T51C-V70C).
experiment_descriptionSynchrotron SAXS data from solutions of uPAR T51C-V70C in 20 mM PBS, 5 %(v/v) glycerol, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2.8 mg/ml were measured at 10°C. 20 successive 0.050 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_unit1/cm
experimental_mw46.108
experimental_mw_errornull
guinier_i0_mw46.108
guinier_i0_mw_error5.0
porod_mw32.0
porod_mw_errornull
pddf_i00.03608
pddf_i0_error0.004
guinier_i00.036
guinier_i0_error0.001
pddf_rg2.592
pddf_rg_error0.02
guinier_rg2.52
guinier_rg_error0.01
pddf_dmax8.9
pddf_dmax_error0.5
porod_volume54.5
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last161
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDF92_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 个字段值
字段路径原始值
codeSASDF92
statussuccess
started_at2026-08-11T13:33:20.099839+00:00
finished_at2026-08-11T13:33:33.618084+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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查看完整 summary.json 原文
{
  "code": "SASDF92",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?",
    "publication": {
      "title": "Did evolution create a flexible ligand-binding cavity in the urokinase receptor through deletion of a plesiotypic disulfide bond?",
      "author_list": "Leth JM, Mertens HDT, Leth-Espensen KZ, Jørgensen TJD, Ploug M",
      "journal": "J Biol Chem",
      "doi": "10.1074/jbc.RA119.007847",
      "pmid": "30894413",
      "published_date": "2019 Mar 20"
    },
    "status": "released",
    "submitted_date": "2019-01-30",
    "released_date": "2019-03-20"
  },
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    "sample": {
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          "long_name": "Urokinase plasminogen activator surface receptor",
          "short_name": "uPAR",
          "sequence": ">sp|Q03405|UPAR_HUMAN Urokinase plasminogen activator surface receptor OS=Homo sapiens GN=PLAUR PE=1 SV=1\nMGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT\n\n",
          "organism": "Homo sapiens",
          "uniprot_code": "Q03405",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MGHPPLLPLLLLLHTCVPASWGLRCMQCKTNGDCRVEECALGQDLCRTTIVRLWEEGEEL\nELVEKSCTHSEKTNRTLSYRTGLKITSLTEVVCGLDLCNQGNSGRAVTYSRSRYLECISC\nGSSDMSCERGRHQSLQCRSPEEQCLDVVTHWIQEGEEGRPKDDRHLRGCGYLPGCPGSNG\nFHNNDTFHFLKCCNTTKCNEGPILELENLPQNGRQCYSCKGNSTHGCSSEETFLIDCRGP\nMNQCLVATGTHEPKNQSYMVRGCATASMCQHAHLGDAFSMNHIDVSCCTKSGCNHPDLDV\nQYRSGAAPQPGPAHLSLTITLLMTARLWGGTLLWT",
          "mw": 36.98,
          "total_mw": 36.98,
          "number_molecules": 1,
          "complex_state": null,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM PBS, 5 %(v/v) glycerol",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Urokinase plasminogen activator surface receptor, uPAR, T51C-V70C",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
          }
        ],
        "contributor_name": "Haydyn",
        "contributor_surname": "Mertens",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2017-12-01",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 0.05,
    "number_of_frames": 20,
    "wavelength": 0.124,
    "sample_detector_distance": 3.1,
    "concentration_min": 0.3,
    "concentration_max": 2.8,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.072,
    "s_max": 5.088,
    "total_exposure_time": null,
    "seccolumn": null
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    {
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDF92_fit1_model1_img.png",
          "software": "DAMMIN",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDF92_fit1_model1.pdb",
          "model_mw": 31.531,
          "bead_radius": 2.5,
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          "symmetry": null,
          "comment": "Refined DAMMIN model from average volume (10 DAMMIF iterations)",
          "user": 12
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/ref_ibuMksD_fit_img.png",
      "software": "DAMMIN",
      "chi_square_value": 0.955,
      "p_value": 0.89146,
      "fit_residual_plot": "ref_ibuMksD_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDF92_fit1.fir",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/ref_DvJhoSj.log",
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      "description": "Refined DAMMIN model from average volume (10 DAMMIF iterations)"
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  "i0_calibration_standard": null,
  "description": "Introduced disulfide in the first LU domain, DI, of uPAR (T51C-V70C).",
  "experiment_description": "Synchrotron SAXS data from solutions of uPAR T51C-V70C in 20 mM PBS, 5 %(v/v) glycerol, pH 7.4 were collected on the EMBL P12 beam line at PETRA III (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2.8 mg/ml were measured at 10°C. 20 successive 0.050 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_unit": "1/cm",
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  "pddf_i0_error": 0.004,
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  "guinier_rg_error": 0.01,
  "pddf_dmax": 8.9,
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  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 161,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDF92_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
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  "finished_at": "2026-08-11T13:33:33.618084+00:00",
  "source_last_modified": "2023-06-21T07:56:39.492710+02:00",
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