SASDA84

RNA Aptamer

数据类型：SASBDB 实验数据 状态：Published 曲线类型：Single concentration 最后更新：2023-05-25T11:22:16.556436+02:00

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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · RNA Aptamer

浓度	— – 0.5 mg/ml	缓冲液 / pH	Hepes / 7.4
Experimental temperature	15.0	设备 / 束线	DORIS III, DESY / EMBL X33
波长	— nm	曝光	120.0 s × 2

分子组分

组分	类型 / Organism	UniProt 与Construct	寡聚状态	Molecular weight
SRB2m 查看序列 GGAACCUCGCUUCGGCGAUGAUGGAGAGGCGCAAGGUUAACCGCCUCAGGUUCC	RNA—	——–—	dimer分子数 2	16.55 kDa

实验曲线

曲线	点数 / 列	q range	误差质量	负强度点	来源文件
1	2086[3]	0.244853–5.07169 1/nm	含误差列缺失 0	341	sasbdb/entries/84/sasda84/source/SASDA84.dat

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2. SASBDB 报告的指标 Reported Results

指标	方法	数值	误差	单位
dmax	P(r)	8.0	—	nm
i0	Guinier	180.23	—	—
i0	P(r)	177.0	—	—
mw	Experimental	20.0	—	kDa
porod_volume	Porod	24.0	—	nm³
rg	Guinier	2.25	—	nm
rg	P(r)	2.27	—	nm

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 · —

χ²：3.265249CorMap p：1.5e-05单位：1/A

拟合数据拟合图残差图

模型	名称 / 类型	软件	Symmetry	模型 MW	PDB 声明	来源文件
1	—dummy	DAMMIN	—	—	—	模型图片

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4. 来源文件索引 Source Files

类别	路径	Download状态	大小
curve	sasbdb/entries/84/sasda84/source/SASDA84.dat	downloaded	95408
full_entry_zip	sasbdb/entries/84/sasda84/source/SASDA84.zip	downloaded	53251
pddf	sasbdb/entries/84/sasda84/source/SASDA84.out	downloaded	41068
sascif	sasbdb/entries/84/sasda84/source/SASDA84.sascif	downloaded	218123
summary	sasbdb/entries/84/sasda84/source/summary.json	downloaded	6311

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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“—”；Not declared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	Hepes	缓冲液浓度	—
pH	7.4	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	2007-10-24	储存 / 测量温度	15.0 / 15.0
曝光时间	120.0	帧数	2
波长	—	样品-探测器距离	—
光源	X-ray synchrotron	探测器	MAR 345 Image Plate
机构 / 束线	DORIS III, DESY / EMBL X33 · Hamburg, Germany
q range	0.245 – 5.072	样品体积 / 流速	— / —

SASBDB 原始图

可Download文件

类别	文件	状态	大小	校验值	Download与查看
curve	sasbdb/entries/84/sasda84/source/SASDA84.dat	downloaded	95408	d75364cf8a8e6aa7bac4102691264d2a441a8a48a49bc213c495894e5c5a19aa	Download查看原文件源站
full_entry_zip	sasbdb/entries/84/sasda84/source/SASDA84.zip	downloaded	53251	0aa63e12f0fc3f564fd19b291de6ea82e3595d4c576650d07930ba5311b76e6c	Download查看原文件源站
pddf	sasbdb/entries/84/sasda84/source/SASDA84.out	downloaded	41068	bf796aa5eac9fd7da0276f8c53785c074c9c391cc7e3442160e271dad56da161	Download查看原文件源站
sascif	sasbdb/entries/84/sasda84/source/SASDA84.sascif	downloaded	218123	feb9d45f1902866e9cc8b2f9971cbf1cec435f552ba43e3c90d9bc00ce8c2430	Download查看原文件源站
summary	sasbdb/entries/84/sasda84/source/summary.json	downloaded	6311	7844556ede09f095f0eaf3405e8d6cbd66d43cc9db3152e0a6ca5fe3a551e982	Download查看原文件源站

curve：来源记录

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  "url": "https://www.sasbdb.org/media/intensities_files/SASDA84.dat"
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full_entry_zip：来源记录与 ZIP 内部目录（4 项）

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  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/zip_directories/SASDA84.zip",
  "zip_member_count": 4,
  "zip_members": [
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      "name": "SASDA84/pddf/SASDA84.out",
      "size": 41068
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    {
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      "name": "SASDA84/SASDA84_fit1.fir",
      "size": 28221
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    {
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      "name": "SASDA84/SASDA84_fit1_model1.pdb",
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pddf：来源记录

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  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/p_of_R_files/SASDA84.out"
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sascif：来源记录

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  "role": "sascif",
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  "size": 218123,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDA84.sascif"
}

summary：来源记录

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  "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDA84/"
}

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
code	SASDA84
status	Published
type_of_curve	Single concentration
angular_unit	1/nm
project.title	Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering.
project.publication.title	Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering.
project.publication.author_list	Werner A, Konarev PV, Svergun DI, Hahn U
project.publication.journal	Anal Biochem
project.publication.doi	10.1016/j.ab.2009.03.018
project.publication.pmid	19303859
project.publication.published_date	2009 Jun 1
project.status	released
project.submitted_date	null
project.released_date	2015-07-07
pddf_data	https://www.sasbdb.org/media/p_of_R_files/SASDA84.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDA84.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA84_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA84_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA84_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA84_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDA84.sascif
experiment.instrument.detector.type	null
experiment.instrument.detector.name	MAR 345 Image Plate
experiment.instrument.detector.resolution	null
experiment.instrument.name	DORIS III, DESY
experiment.instrument.city	Hamburg
experiment.instrument.country	Germany
experiment.instrument.beamline_name	EMBL X33
experiment.instrument.beam_geometry	null
experiment.instrument.type_of_source	X-ray synchrotron
experiment.instrument.point_source	null
experiment.instrument.line_collimation	null
experiment.instrument.sample_path_length	null
experiment.instrument.line_collimation_slitlength	null
experiment.instrument.line_collimation_integrationwidth	null
experiment.instrument.xray_energy	null
experiment.instrument.beam_profile_ah	null
experiment.instrument.beam_profile_al	null
experiment.sample.molecule[0].long_name	SRB2m
experiment.sample.molecule[0].short_name	SRB2m
experiment.sample.molecule[0].sequence	GGAACCUCGCUUCGGCGAUGAUGGAGAGGC GCAAGGUUAACCGCCUCAGGUUCC
experiment.sample.molecule[0].organism	null
experiment.sample.molecule[0].uniprot_code	null
experiment.sample.molecule[0].uniprot_range_first	null
experiment.sample.molecule[0].uniprot_range_last	null
experiment.sample.molecule[0].oligomerization	dimer
experiment.sample.molecule[0].molecular_type	RNA
experiment.sample.molecule[0].uniprot_sequence	null
experiment.sample.molecule[0].mw	16.55
experiment.sample.molecule[0].total_mw	33.1
experiment.sample.molecule[0].number_molecules	2
experiment.sample.molecule[0].complex_state	null
experiment.sample.molecule[0].deuteration	null
experiment.sample.molecule[0].molecule_source	biological
experiment.sample.molecule[0].molecule_description	null
experiment.sample.buffer.name	Hepes
experiment.sample.buffer.concentration_unit	null
experiment.sample.buffer.comment	null
experiment.sample.buffer.additive	null
experiment.sample.buffer.concentration	null
experiment.sample.buffer.pka	null
experiment.sample.buffer.ph	7.4
experiment.sample.buffer.deuteration	null
experiment.sample.purity_method	null
experiment.sample.name	RNA Aptamer
experiment.sample.ext_coefficient	null
experiment.sample.contrast	null
experiment.sample.specific_vol	null
experiment.sample.dry_vol	null
experiment.sample.absorbption	null
experiment.sample.deuteration	null
experiment.sample.mixture	null
experiment.contributor[0].affiliation[0].short_name	EMBL-Hamburg
experiment.contributor[0].affiliation[0].address	Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_name	European Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpage	http://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_name	Petr
experiment.contributor[0].contributor_surname	Konarev
experiment.contributor[0].orcid	null
experiment.concentration_method	null
experiment.concentration_unit	mg/ml
experiment.date	2007-10-24
experiment.storage_temperature	15.0
experiment.cell_temperature	15.0
experiment.exposure_time	120.0
experiment.number_of_frames	2
experiment.wavelength	null
experiment.sample_detector_distance	null
experiment.concentration_min	null
experiment.concentration_max	0.5
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.245
experiment.s_max	5.072
experiment.total_exposure_time	null
experiment.seccolumn	null
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDA84_fit1_model1_img.png
fits[0].models[0].software	DAMMIN
fits[0].models[0].pdb_link	[]
fits[0].models[0].model_title	null
fits[0].models[0].type_of_model	dummy
fits[0].models[0].software_version
fits[0].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDA84_fit1_model1.pdb
fits[0].models[0].model_mw	null
fits[0].models[0].bead_radius	null
fits[0].models[0].log	null
fits[0].models[0].symmetry
fits[0].models[0].comment
fits[0].models[0].user	88
fits[0].fit_unit	1/A
fits[0].fit_plot	https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDA84_fit1_fit_img.png
fits[0].software	null
fits[0].chi_square_value	3.265249
fits[0].p_value	1.5e-05
fits[0].fit_residual_plot	SASDA84_fit1_fitresiduals_img.png
fits[0].fit_data	https://www.sasbdb.org/media/fitting_files/SASDA84_fit1.fir
fits[0].fit_log	null
fits[0].software_version	null
fits[0].description	null
estimated_volume_method	null
pddf_software	ATSAS GNOM
pddf_software_version	GNOM
i0_calibration_standard	null
description	null
experiment_description	null
tags[0]	X33
intensity_unit	null
experimental_mw	20.0
experimental_mw_error	null
guinier_i0_mw	null
guinier_i0_mw_error	null
porod_mw	null
porod_mw_error	null
pddf_i0	177.0
pddf_i0_error	null
guinier_i0	180.23
guinier_i0_error	null
pddf_rg	2.27
pddf_rg_error	null
guinier_rg	2.25
guinier_rg_error	null
pddf_dmax	8.0
pddf_dmax_error	null
porod_volume	24.0
porod_volume_error	null
estimated_volume	null
estimated_volume_error	null
guinier_point_first	null
guinier_point_last	null
pddf_point_first	null
pddf_point_last	null
i0_calibration_standard_data	null
intensities_log_log_plot	SASDA84_datloglog_img.png
symmetry	null
last_modified	2023-05-25T11:22:16.556436+02:00
bragg_peak	[]

manifest.json：36 个字段值

字段路径	原始值
code	SASDA84
status	success
started_at	2026-08-11T14:15:52.635960+00:00
finished_at	2026-08-11T14:16:01.562019+00:00
source_last_modified	2023-05-25T11:22:16.556436+02:00
files[0].status	downloaded
files[0].url	https://www.sasbdb.org/rest-api/entry/summary/SASDA84/
files[0].path	/data/saxsdb/sasbdb/entries/84/sasda84/source/summary.json
files[0].size	6311
files[0].sha256	7844556ede09f095f0eaf3405e8d6cbd66d43cc9db3152e0a6ca5fe3a551e982
files[1].status	downloaded
files[1].url	https://www.sasbdb.org/media/intensities_files/SASDA84.dat
files[1].path	/data/saxsdb/sasbdb/entries/84/sasda84/source/SASDA84.dat
files[1].size	95408
files[1].sha256	d75364cf8a8e6aa7bac4102691264d2a441a8a48a49bc213c495894e5c5a19aa
files[1].role	curve
files[2].status	downloaded
files[2].url	https://www.sasbdb.org/media/p_of_R_files/SASDA84.out
files[2].path	/data/saxsdb/sasbdb/entries/84/sasda84/source/SASDA84.out
files[2].size	41068
files[2].sha256	bf796aa5eac9fd7da0276f8c53785c074c9c391cc7e3442160e271dad56da161
files[2].role	pddf
files[3].status	downloaded
files[3].url	https://www.sasbdb.org/media/sascif/sascif_files/SASDA84.sascif
files[3].path	/data/saxsdb/sasbdb/entries/84/sasda84/source/SASDA84.sascif
files[3].size	218123
files[3].sha256	feb9d45f1902866e9cc8b2f9971cbf1cec435f552ba43e3c90d9bc00ce8c2430
files[3].role	sascif
files[4].status	downloaded
files[4].url	https://www.sasbdb.org/media/zip_directories/SASDA84.zip
files[4].path	/data/saxsdb/sasbdb/entries/84/sasda84/source/SASDA84.zip
files[4].size	53251
files[4].sha256	0aa63e12f0fc3f564fd19b291de6ea82e3595d4c576650d07930ba5311b76e6c
files[4].role	full_entry_zip
files[4].zip_member_count	4
files[4].zip_validation	central_directory_readable

查看完整 summary.json 原文

{
  "code": "SASDA84",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering.",
    "publication": {
      "title": "Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering.",
      "author_list": "Werner A, Konarev PV, Svergun DI, Hahn U",
      "journal": "Anal Biochem",
      "doi": "10.1016/j.ab.2009.03.018",
      "pmid": "19303859",
      "published_date": "2009 Jun 1"
    },
    "status": "released",
    "submitted_date": null,
    "released_date": "2015-07-07"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDA84.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDA84.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA84_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA84_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDA84_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDA84_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDA84.sascif",
  "experiment": {
    "instrument": {
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        "name": "MAR 345 Image Plate",
        "resolution": null
      },
      "name": "DORIS III, DESY",
      "city": "Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL X33",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
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      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "SRB2m",
          "short_name": "SRB2m",
          "sequence": "GGAACCUCGCUUCGGCGAUGAUGGAGAGGC\r\nGCAAGGUUAACCGCCUCAGGUUCC",
          "organism": null,
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
          "molecular_type": "RNA",
          "uniprot_sequence": null,
          "mw": 16.55,
          "total_mw": 33.1,
          "number_molecules": 2,
          "complex_state": null,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "Hepes",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "RNA Aptamer",
      "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": "Petr",
        "contributor_surname": "Konarev",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": "mg/ml",
    "date": "2007-10-24",
    "storage_temperature": 15.0,
    "cell_temperature": 15.0,
    "exposure_time": 120.0,
    "number_of_frames": 2,
    "wavelength": null,
    "sample_detector_distance": null,
    "concentration_min": null,
    "concentration_max": 0.5,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.245,
    "s_max": 5.072,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
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          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
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查看完整 manifest.json 原文

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Title	Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering.
作者	Werner A, Konarev PV, Svergun DI, Hahn U
DOI / PMID	10.1016/j.ab.2009.03.018 / 19303859