SASDCK8

Lysozyme (WAXS)

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
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Lysozyme (WAXS)

浓度19.4 – 25.1 缓冲液 / pH40 mM Sodium Acetate pH 4.0, 50 mM NaCl / 4.0
实验温度20.0 设备 / 束线PETRA III / EMBL P12
波长0.062 nm曝光0.1 s × —

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Lysozyme C
查看序列
KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
proteinGallus gallusP0069819–147monomer分子数 114.31 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
11914[3]0.241516–17.8562 1/nm含误差列缺失 011sasbdb/entries/k8/sasdck8/source/SASDCK8.dat
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2. SASBDB 报告的指标 Reported Results

指标方法数值误差单位
i0Guinier648.360.93arbitrary
mwExperimental12.0—kDa
rgGuinier1.410.03nm

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40 mM Sodium Acetate pH 4.0, 50 mM NaCl缓冲液浓度—
pH4.0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2015-05-31储存 / 测量温度20.0 / 20.0
曝光时间0.1帧数—
波长0.062样品-探测器距离1.5
光源X-ray synchrotron探测器Pilatus 2M
机构 / 束线PETRA III / EMBL P12 · DESY; Hamburg, Germany
q 范围0.242 – 17.856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

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/k8/sasdck8/source/SASDCK8.zipdownloaded862205fa561c0e69b31dfbeff67ae2914ef29ef404c8981cbfd7b5a6d7ebdb181e392下载查看原文件源站
pddfsasbdb/entries/k8/sasdck8/source/SASDCK8.outnot_listed——下载查看原文件
sascifsasbdb/entries/k8/sasdck8/source/SASDCK8.sascifdownloaded314260cc8bd38bb81ec0b469b6b743fde77bfd7b8cc9a28b916fef222a7c6e4f2ceabe下载查看原文件源站
summarysasbdb/entries/k8/sasdck8/source/summary.jsondownloaded7084663b6993115d16e3dceedceba25056628e12eff0d30328a4e7a97af8e1810ccd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(3 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:154 个字段值
字段路径原始值
codeSASDCK8
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleWAXS benchmark on standard proteins
project.publicationnull
project.statusreleased
project.submitted_date2017-10-17
project.released_date2021-09-13
pddf_datanull
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDCK8.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK8_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK8_kratky_img.png
pddf_plotnull
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK8_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDCK8.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_nameLysozyme C
experiment.sample.molecule[0].short_nameLysozyme, lys
experiment.sample.molecule[0].sequenceKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG NGMNAWVAWRNRCKGTDVQAWIRGCRL
experiment.sample.molecule[0].organismGallus gallus
experiment.sample.molecule[0].uniprot_codeP00698
experiment.sample.molecule[0].uniprot_range_first19
experiment.sample.molecule[0].uniprot_range_last147
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG NGMNAWVAWRNRCKGTDVQAWIRGCRL
experiment.sample.molecule[0].mw14.31
experiment.sample.molecule[0].total_mw14.31
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_description
experiment.sample.buffer.name40 mM Sodium Acetate pH 4.0, 50 mM NaCl
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph4.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameLysozyme (WAXS)
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_nameMaxim
experiment.contributor[0].contributor_surnamePetoukhov
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-05-31
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time0.1
experiment.number_of_framesnull
experiment.wavelength0.062
experiment.sample_detector_distance1.5
experiment.concentration_min19.4
experiment.concentration_max25.1
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.242
experiment.s_max17.856
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDCK8_fit1_model1_img.png
fits[0].models[0].softwarePDB (Protein Data Bank)
fits[0].models[0].pdb_link[0].pdb_code6lyz
fits[0].models[0].pdb_link[0].ext_code6LYZ
fits[0].models[0].pdb_link[0].ext_typepdb
fits[0].models[0].pdb_link[0].difference_with_modelidentical
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_version
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDCK8_fit1_model1.pdb
fits[0].models[0].model_mw14.32
fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetry
fits[0].models[0].comment
fits[0].models[0].user102
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value2.05
fits[0].p_value0.0
fits[0].fit_residual_plotSASDCK8_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDCK8_fit1.fit
fits[0].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/6lyz04.log
fits[0].software_versioncrysol 3.0
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwarenull
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of lysozyme in 40 mM sodium acetate, 50 mM NaCl, pH 4 were collected on the EMBL-P12 beam line at the PETRA III storage ring (Hamburg, Germany), using a Pilatus 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.062 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 19.4 and 25.1 mg/ml were measured at 20°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the data scaled to protein concentration. 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[0]benchmark
intensity_unitarbitrary
experimental_mw12.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i0null
pddf_i0_errornull
guinier_i0648.36
guinier_i0_error0.93
pddf_rgnull
pddf_rg_errornull
guinier_rg1.41
guinier_rg_error0.03
pddf_dmaxnull
pddf_dmax_errornull
porod_volumenull
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last58
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCK8_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:33 个字段值
字段路径原始值
codeSASDCK8
statussuccess
started_at2026-08-11T15:54:56.596019+00:00
finished_at2026-08-11T15:55:03.503488+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
files[0].statusdownloaded
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files[0].size7084
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files[1].path/data/saxsdb/sasbdb/entries/k8/sasdck8/source/SASDCK8.dat
files[1].size89954
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files[4].zip_validationcentral_directory_readable
查看完整 summary.json 原文
{
  "code": "SASDCK8",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "WAXS benchmark on standard proteins",
    "publication": null,
    "status": "released",
    "submitted_date": "2017-10-17",
    "released_date": "2021-09-13"
  },
  "pddf_data": null,
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCK8.dat",
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      "country": "Germany",
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    },
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          "molecule_description": ""
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        ],
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        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-05-31",
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    "exposure_time": 0.1,
    "number_of_frames": null,
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    "flow_rate": null,
    "s_min": 0.242,
    "s_max": 17.856,
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              "ext_code": "6LYZ",
              "ext_type": "pdb",
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            }
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          "software_version": "",
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          "bead_radius": 1.9,
          "log": null,
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          "user": 102
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDCK8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
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}
查看完整 manifest.json 原文
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