SASDAT7

Aptamer AIR-3 5FU

数据类型：SASBDB 实验数据 状态：Published 曲线类型：Single concentration 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 · Aptamer AIR-3 5FU

浓度	— – 0.3 mg/ml	缓冲液 / pH	water / 7.5
实验温度	10.0	设备 / 束线	PETRA III / EMBL P12
波长	0.12 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
AIR3-5FU 查看序列 GGAAGAAAGAGGUCUGAGACAUUCUCUUAUAGGGGAGGCUGUGGUGAGGGAAUAUUAAGAGAAUUAACGGUCUAGUUCACCUCGACUUCUGGAGUUGACGUUGCUU	RNA—	——–—	dimer分子数 2	34.39 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
1	1694[3]	0.0290642–4.48844 1/nm	含误差列缺失 0	297	sasbdb/entries/t7/sasdat7/source/SASDAT7.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)	16.0	0.5	nm
i0	Guinier	18200.0	—	—
i0	P(r)	19290.0	—	—
mw	Experimental	77.0	—	kDa
mw	Porod	77.0	—	kDa
porod_volume	Porod	77.0	—	nm³
rg	Guinier	4.3	0.3	nm
rg	P(r)	4.8	0.3	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 · —

χ²：1.426462CorMap p：0.132656单位：1/A

拟合数据拟合图残差图

模型	名称 / 类型	软件	对称性	模型 MW	PDB 声明	来源文件
1	—dummy	DAMMIF	P1	—	—	模型图片

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4. 来源文件索引 Source Files

类别	路径	下载状态	大小
curve	sasbdb/entries/t7/sasdat7/source/SASDAT7.dat	downloaded	76508
full_entry_zip	sasbdb/entries/t7/sasdat7/source/SASDAT7.zip	downloaded	39687
pddf	sasbdb/entries/t7/sasdat7/source/SASDAT7.out	downloaded	27933
sascif	sasbdb/entries/t7/sasdat7/source/SASDAT7.sascif	downloaded	175370
summary	sasbdb/entries/t7/sasdat7/source/summary.json	downloaded	6347

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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	water	缓冲液浓度	—
pH	7.5	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	2013-10-31	储存 / 测量温度	10.0 / 10.0
曝光时间	0.05	帧数	20
波长	0.12	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	0.029 – 4.488	样品体积 / 流速	— / —

SASBDB 原始图

可下载文件

类别	文件	状态	大小	校验值	下载与查看
curve	sasbdb/entries/t7/sasdat7/source/SASDAT7.dat	downloaded	76508	23cc8c84a159ee232413359e99d75f0ba12498ad8e5fdafa6c490a9cb7cf7c4b	下载查看原文件源站
full_entry_zip	sasbdb/entries/t7/sasdat7/source/SASDAT7.zip	downloaded	39687	0f9877bdce9a72d5131e67975a562bdc6509293958abc8cca6ee502e97f26c6c	下载查看原文件源站
pddf	sasbdb/entries/t7/sasdat7/source/SASDAT7.out	downloaded	27933	dc81fcea8be3d77e9a12176d28edaab57beb5146c2d80d434dee15bead089340	下载查看原文件源站
sascif	sasbdb/entries/t7/sasdat7/source/SASDAT7.sascif	downloaded	175370	997c81c52f8e8f731c3158c1e80c193600fd3371ff0d25ea6844d0baf6d44f23	下载查看原文件源站
summary	sasbdb/entries/t7/sasdat7/source/summary.json	downloaded	6347	f9bbc380ae7da6f163e362893e16b0fc18bc2533b8561849a73fc422d9c33200	下载查看原文件源站

curve：来源记录

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  "role": "curve",
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  "size": 76508,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/intensities_files/SASDAT7.dat"
}

full_entry_zip：来源记录与 ZIP 内部目录（4 项）

{
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  "size": 39687,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/zip_directories/SASDAT7.zip",
  "zip_member_count": 4,
  "zip_members": [
    {
      "crc32": "7a1bce84",
      "name": "SASDAT7/experimental_data/SASDAT7.dat",
      "size": 76508
    },
    {
      "crc32": "7cd5b455",
      "name": "SASDAT7/pddf/SASDAT7.out",
      "size": 27933
    },
    {
      "crc32": "f13eb6d4",
      "name": "SASDAT7/SASDAT7_fit1.fir",
      "size": 17103
    },
    {
      "crc32": "d5b78dba",
      "name": "SASDAT7/SASDAT7_fit1_model1.pdb",
      "size": 34257
    }
  ],
  "zip_validation": "central_directory_readable"
}

pddf：来源记录

{
  "path": "/data/saxsdb/sasbdb/entries/t7/sasdat7/source/SASDAT7.out",
  "role": "pddf",
  "sha256": "dc81fcea8be3d77e9a12176d28edaab57beb5146c2d80d434dee15bead089340",
  "size": 27933,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/p_of_R_files/SASDAT7.out"
}

sascif：来源记录

{
  "path": "/data/saxsdb/sasbdb/entries/t7/sasdat7/source/SASDAT7.sascif",
  "role": "sascif",
  "sha256": "997c81c52f8e8f731c3158c1e80c193600fd3371ff0d25ea6844d0baf6d44f23",
  "size": 175370,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAT7.sascif"
}

summary：来源记录

{
  "path": "/data/saxsdb/sasbdb/entries/t7/sasdat7/source/summary.json",
  "sha256": "f9bbc380ae7da6f163e362893e16b0fc18bc2533b8561849a73fc422d9c33200",
  "size": 6347,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDAT7/"
}

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	SASDAT7
status	Published
type_of_curve	Single concentration
angular_unit	1/nm
project.title	Structure and target interaction of a G-quadruplex RNA-aptamer.
project.publication.title	Structure and target interaction of a G-quadruplex RNA-aptamer.
project.publication.author_list	Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
project.publication.journal	RNA Biol
project.publication.doi	10.1080/15476286.2016.1212151
project.publication.pmid	27471797
project.publication.published_date	2016 Oct 2
project.status	released
project.submitted_date	null
project.released_date	2016-09-08
pddf_data	https://www.sasbdb.org/media/p_of_R_files/SASDAT7.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDAT7.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT7_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT7_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAT7_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT7_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDAT7.sascif
experiment.instrument.detector.type	null
experiment.instrument.detector.name	Pilatus 2M
experiment.instrument.detector.resolution	null
experiment.instrument.name	PETRA III
experiment.instrument.city	DESY; Hamburg
experiment.instrument.country	Germany
experiment.instrument.beamline_name	EMBL P12
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	AIR3-5FU
experiment.sample.molecule[0].short_name	null
experiment.sample.molecule[0].sequence	GGAAGAAAGAGGUCUGAGACAUUCUCUUAUAGGGGAGGCUGUGGUGAGGGAAUAUUAAGAGAAUUAACGGUCUAGUUCACCUCGACUUCUGGAGUUGACGUUGCUU
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	34.39
experiment.sample.molecule[0].total_mw	68.781
experiment.sample.molecule[0].number_molecules	2
experiment.sample.molecule[0].complex_state	False
experiment.sample.molecule[0].deuteration	null
experiment.sample.molecule[0].molecule_source	biological
experiment.sample.molecule[0].molecule_description	null
experiment.sample.buffer.name	water
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	7.5
experiment.sample.buffer.deuteration	null
experiment.sample.purity_method	null
experiment.sample.name	Aptamer AIR-3 5FU
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	Erica
experiment.contributor[0].contributor_surname	Valentini
experiment.contributor[0].orcid	null
experiment.concentration_method	null
experiment.concentration_unit	mg/ml
experiment.date	2013-10-31
experiment.storage_temperature	10.0
experiment.cell_temperature	10.0
experiment.exposure_time	0.05
experiment.number_of_frames	20
experiment.wavelength	0.12
experiment.sample_detector_distance	3.1
experiment.concentration_min	null
experiment.concentration_max	0.3
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.029
experiment.s_max	4.488
experiment.total_exposure_time	null
experiment.seccolumn	null
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDAT7_fit1_model1_img.png
fits[0].models[0].software	DAMMIF
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/SASDAT7_fit1_model1.pdb
fits[0].models[0].model_mw	null
fits[0].models[0].bead_radius	3.5
fits[0].models[0].log	null
fits[0].models[0].symmetry	P1
fits[0].models[0].comment
fits[0].models[0].user	1
fits[0].fit_unit	1/A
fits[0].fit_plot	https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAT7_fit1_fit_img.png
fits[0].software	null
fits[0].chi_square_value	1.426462
fits[0].p_value	0.132656
fits[0].fit_residual_plot	SASDAT7_fit1_fitresiduals_img.png
fits[0].fit_data	https://www.sasbdb.org/media/fitting_files/SASDAT7_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	null
i0_calibration_standard	null
description	null
experiment_description	null
tags	[]
intensity_unit	null
experimental_mw	77.0
experimental_mw_error	null
guinier_i0_mw	null
guinier_i0_mw_error	null
porod_mw	77.0
porod_mw_error	null
pddf_i0	19290.0
pddf_i0_error	null
guinier_i0	18200.0
guinier_i0_error	null
pddf_rg	4.8
pddf_rg_error	0.3
guinier_rg	4.3
guinier_rg_error	0.3
pddf_dmax	16.0
pddf_dmax_error	0.5
porod_volume	77.0
porod_volume_error	null
estimated_volume	null
estimated_volume_error	null
guinier_point_first	76
guinier_point_last	104
pddf_point_first	null
pddf_point_last	null
i0_calibration_standard_data	null
intensities_log_log_plot	SASDAT7_datloglog_img.png
symmetry	null
last_modified	2023-06-21T07:56:39.492710+02:00
bragg_peak	[]

manifest.json：36 个字段值

字段路径	原始值
code	SASDAT7
status	success
started_at	2026-08-11T15:38:34.896960+00:00
finished_at	2026-08-11T15:38:43.119573+00:00
source_last_modified	2023-06-21T07:56:39.492710+02:00
files[0].status	downloaded
files[0].url	https://www.sasbdb.org/rest-api/entry/summary/SASDAT7/
files[0].path	/data/saxsdb/sasbdb/entries/t7/sasdat7/source/summary.json
files[0].size	6347
files[0].sha256	f9bbc380ae7da6f163e362893e16b0fc18bc2533b8561849a73fc422d9c33200
files[1].status	downloaded
files[1].url	https://www.sasbdb.org/media/intensities_files/SASDAT7.dat
files[1].path	/data/saxsdb/sasbdb/entries/t7/sasdat7/source/SASDAT7.dat
files[1].size	76508
files[1].sha256	23cc8c84a159ee232413359e99d75f0ba12498ad8e5fdafa6c490a9cb7cf7c4b
files[1].role	curve
files[2].status	downloaded
files[2].url	https://www.sasbdb.org/media/p_of_R_files/SASDAT7.out
files[2].path	/data/saxsdb/sasbdb/entries/t7/sasdat7/source/SASDAT7.out
files[2].size	27933
files[2].sha256	dc81fcea8be3d77e9a12176d28edaab57beb5146c2d80d434dee15bead089340
files[2].role	pddf
files[3].status	downloaded
files[3].url	https://www.sasbdb.org/media/sascif/sascif_files/SASDAT7.sascif
files[3].path	/data/saxsdb/sasbdb/entries/t7/sasdat7/source/SASDAT7.sascif
files[3].size	175370
files[3].sha256	997c81c52f8e8f731c3158c1e80c193600fd3371ff0d25ea6844d0baf6d44f23
files[3].role	sascif
files[4].status	downloaded
files[4].url	https://www.sasbdb.org/media/zip_directories/SASDAT7.zip
files[4].path	/data/saxsdb/sasbdb/entries/t7/sasdat7/source/SASDAT7.zip
files[4].size	39687
files[4].sha256	0f9877bdce9a72d5131e67975a562bdc6509293958abc8cca6ee502e97f26c6c
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": "SASDAT7",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Structure and target interaction of a G-quadruplex RNA-aptamer.",
    "publication": {
      "title": "Structure and target interaction of a G-quadruplex RNA-aptamer.",
      "author_list": "Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U",
      "journal": "RNA Biol",
      "doi": "10.1080/15476286.2016.1212151",
      "pmid": "27471797",
      "published_date": "2016 Oct 2"
    },
    "status": "released",
    "submitted_date": null,
    "released_date": "2016-09-08"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAT7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAT7.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT7_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT7_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAT7_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAT7_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAT7.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "AIR3-5FU",
          "short_name": null,
          "sequence": "GGAAGAAAGAGGUCUGAGACAUUCUCUUAUAGGGGAGGCUGUGGUGAGGGAAUAUUAAGAGAAUUAACGGUCUAGUUCACCUCGACUUCUGGAGUUGACGUUGCUU",
          "organism": null,
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
          "molecular_type": "RNA",
          "uniprot_sequence": null,
          "mw": 34.39,
          "total_mw": 68.781,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "water",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Aptamer AIR-3 5FU",
      "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": "Erica",
        "contributor_surname": "Valentini",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": "mg/ml",
    "date": "2013-10-31",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 0.05,
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查看完整 manifest.json 原文

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标题	Structure and target interaction of a G-quadruplex RNA-aptamer.
作者	Szameit K, Berg K, Kruspe S, Valentini E, Magbanua E, Kwiatkowski M, Chauvot de Beauchêne I, Krichel B, Schamoni K, Uetrecht C, Svergun DI, Schlüter H, Zacharias M, Hahn U
DOI / PMID	10.1080/15476286.2016.1212151 / 27471797