SASDAV7

Aptamer AIR-3A

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-3A

浓度	— – 0.4 mg/ml	缓冲液 / pH	water / 7.5
Experimental temperature	10.0	设备 / 束线	PETRA III / EMBL P12
波长	0.12 nm	曝光	0.05 s × —

分子组分

组分	类型 / Organism	UniProt 与Construct	寡聚状态	Molecular weight
AIR-3A 查看序列 GGGGAGGCUGUGGUGAGGG	RNA—	——–—	dimer分子数 2	6.388 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	1682[3]	0.027543–4.45043 1/nm	含误差列缺失 0	175	sasbdb/entries/v7/sasdav7/source/SASDAV7.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)	6.5	—	nm
i0	Guinier	1690.0	—	—
i0	P(r)	1666.0	—	—
mw	Experimental	14.0	—	kDa
mw	Porod	14.0	—	kDa
porod_volume	Porod	14.0	—	nm³
rg	Guinier	1.9	—	nm
rg	P(r)	1.9	—	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 · —

χ²：1.249924CorMap p：0.000227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	P2	—	—	模型图片

拟合 2 · —

χ²：1.087849CorMap p：0.047327单位：1/A

拟合数据拟合图

模型	名称 / 类型	软件	Symmetry	模型 MW	PDB 声明	来源文件
1	—atomic	SASREF	P2	12.7	—	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/v7/sasdav7/source/SASDAV7.dat	downloaded	75965
full_entry_zip	sasbdb/entries/v7/sasdav7/source/SASDAV7.zip	downloaded	78974
pddf	sasbdb/entries/v7/sasdav7/source/SASDAV7.out	downloaded	41251
sascif	sasbdb/entries/v7/sasdav7/source/SASDAV7.sascif	downloaded	398762
summary	sasbdb/entries/v7/sasdav7/source/summary.json	downloaded	7265

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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	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	2013-12-06	储存 / 测量温度	10.0 / 10.0
曝光时间	0.05	帧数	—
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 range	0.028 – 4.45	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/v7/sasdav7/source/SASDAV7.dat	downloaded	75965	75e6c26c7fd1ea41bf302ad335135009f68fb91776aa9b961eef0992cd67113d	Download查看原文件源站
full_entry_zip	sasbdb/entries/v7/sasdav7/source/SASDAV7.zip	downloaded	78974	879ff9a2110b787e9951f77ae84ba4e7f8b9c2845adf033591b81702001f72eb	Download查看原文件源站
pddf	sasbdb/entries/v7/sasdav7/source/SASDAV7.out	downloaded	41251	f42655f922f8b6919e549219fcbafe9311438add628461b4c03e2eb7f5d8a96a	Download查看原文件源站
sascif	sasbdb/entries/v7/sasdav7/source/SASDAV7.sascif	downloaded	398762	b70eced1c88f0899fc3f2ac3331e162f7b1232d9c8f3b629e8b3842f78d2f7af	Download查看原文件源站
summary	sasbdb/entries/v7/sasdav7/source/summary.json	downloaded	7265	ba48170a8f5b969b6783faf08372cdb9059e9614ffe6047ac1d4b09a3bc44276	Download查看原文件源站

curve：来源记录

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  "role": "curve",
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  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/intensities_files/SASDAV7.dat"
}

full_entry_zip：来源记录与 ZIP 内部目录（6 项）

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  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/zip_directories/SASDAV7.zip",
  "zip_member_count": 6,
  "zip_members": [
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    {
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      "name": "SASDAV7/pddf/SASDAV7.out",
      "size": 41251
    },
    {
      "crc32": "fb1ad2a3",
      "name": "SASDAV7/SASDAV7_fit1.fir",
      "size": 26844
    },
    {
      "crc32": "bcadf526",
      "name": "SASDAV7/SASDAV7_fit1_model1.pdb",
      "size": 64369
    },
    {
      "crc32": "f1fffbcf",
      "name": "SASDAV7/SASDAV7_fit2.fit",
      "size": 68919
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    {
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pddf：来源记录

{
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  "role": "pddf",
  "sha256": "f42655f922f8b6919e549219fcbafe9311438add628461b4c03e2eb7f5d8a96a",
  "size": 41251,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/p_of_R_files/SASDAV7.out"
}

sascif：来源记录

{
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  "role": "sascif",
  "sha256": "b70eced1c88f0899fc3f2ac3331e162f7b1232d9c8f3b629e8b3842f78d2f7af",
  "size": 398762,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAV7.sascif"
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summary：来源记录

{
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  "size": 7265,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDAV7/"
}

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：179 个字段值

字段路径	原始值
code	SASDAV7
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/SASDAV7.out
intensities_data	https://www.sasbdb.org/media/intensities_files/SASDAV7.dat
intensities_log_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV7_dat_img.png
intensities_kratky_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV7_kratky_img.png
pddf_plot	https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAV7_pofr_img.png
intensities_guinier_plot	https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV7_guinier_img.png
sascif_data	https://www.sasbdb.org/media/sascif/sascif_files/SASDAV7.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	AIR-3A
experiment.sample.molecule[0].short_name	null
experiment.sample.molecule[0].sequence	GGGGAGGCUGUGGUGAGGG
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	6.388
experiment.sample.molecule[0].total_mw	12.776
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-3A
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	2013-12-06
experiment.storage_temperature	10.0
experiment.cell_temperature	10.0
experiment.exposure_time	0.05
experiment.number_of_frames	null
experiment.wavelength	0.12
experiment.sample_detector_distance	3.1
experiment.concentration_min	null
experiment.concentration_max	0.4
experiment.sample_volume	null
experiment.flow_rate	null
experiment.s_min	0.028
experiment.s_max	4.45
experiment.total_exposure_time	null
experiment.seccolumn	null
fits[0].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDAV7_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/SASDAV7_fit1_model1.pdb
fits[0].models[0].model_mw	null
fits[0].models[0].bead_radius	1.6
fits[0].models[0].log	null
fits[0].models[0].symmetry	P2
fits[0].models[0].comment	Prolate, Across
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/SASDAV7_fit1_fit_img.png
fits[0].software	null
fits[0].chi_square_value	1.249924
fits[0].p_value	0.000227
fits[0].fit_residual_plot	SASDAV7_fit1_fitresiduals_img.png
fits[0].fit_data	https://www.sasbdb.org/media/fitting_files/SASDAV7_fit1.fir
fits[0].fit_log	null
fits[0].software_version	null
fits[0].description	null
fits[1].models[0].model_plot	https://www.sasbdb.org/media/pdb_file/images/SASDAV7_fit2_model1_img.png
fits[1].models[0].software	SASREF
fits[1].models[0].pdb_link	[]
fits[1].models[0].model_title	null
fits[1].models[0].type_of_model	atomic
fits[1].models[0].software_version
fits[1].models[0].model_data	https://www.sasbdb.org/media/pdb_file/SASDAV7_fit2_model1.pdb
fits[1].models[0].model_mw	12.7
fits[1].models[0].bead_radius	null
fits[1].models[0].log	null
fits[1].models[0].symmetry	P2
fits[1].models[0].comment	Manual made model
fits[1].models[0].user	1
fits[1].fit_unit	1/A
fits[1].fit_plot	https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAV7_fit2_fit_img.png
fits[1].software	null
fits[1].chi_square_value	1.087849
fits[1].p_value	0.047327
fits[1].fit_residual_plot	null
fits[1].fit_data	https://www.sasbdb.org/media/fitting_files/SASDAV7_fit2.fit
fits[1].fit_log	null
fits[1].software_version	null
fits[1].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	14.0
experimental_mw_error	null
guinier_i0_mw	null
guinier_i0_mw_error	null
porod_mw	14.0
porod_mw_error	null
pddf_i0	1666.0
pddf_i0_error	null
guinier_i0	1690.0
guinier_i0_error	null
pddf_rg	1.9
pddf_rg_error	null
guinier_rg	1.9
guinier_rg_error	null
pddf_dmax	6.5
pddf_dmax_error	null
porod_volume	14.0
porod_volume_error	null
estimated_volume	null
estimated_volume_error	null
guinier_point_first	95
guinier_point_last	250
pddf_point_first	null
pddf_point_last	null
i0_calibration_standard_data	null
intensities_log_log_plot	SASDAV7_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	SASDAV7
status	success
started_at	2026-08-11T15:40:33.950605+00:00
finished_at	2026-08-11T15:40:42.718352+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/SASDAV7/
files[0].path	/data/saxsdb/sasbdb/entries/v7/sasdav7/source/summary.json
files[0].size	7265
files[0].sha256	ba48170a8f5b969b6783faf08372cdb9059e9614ffe6047ac1d4b09a3bc44276
files[1].status	downloaded
files[1].url	https://www.sasbdb.org/media/intensities_files/SASDAV7.dat
files[1].path	/data/saxsdb/sasbdb/entries/v7/sasdav7/source/SASDAV7.dat
files[1].size	75965
files[1].sha256	75e6c26c7fd1ea41bf302ad335135009f68fb91776aa9b961eef0992cd67113d
files[1].role	curve
files[2].status	downloaded
files[2].url	https://www.sasbdb.org/media/p_of_R_files/SASDAV7.out
files[2].path	/data/saxsdb/sasbdb/entries/v7/sasdav7/source/SASDAV7.out
files[2].size	41251
files[2].sha256	f42655f922f8b6919e549219fcbafe9311438add628461b4c03e2eb7f5d8a96a
files[2].role	pddf
files[3].status	downloaded
files[3].url	https://www.sasbdb.org/media/sascif/sascif_files/SASDAV7.sascif
files[3].path	/data/saxsdb/sasbdb/entries/v7/sasdav7/source/SASDAV7.sascif
files[3].size	398762
files[3].sha256	b70eced1c88f0899fc3f2ac3331e162f7b1232d9c8f3b629e8b3842f78d2f7af
files[3].role	sascif
files[4].status	downloaded
files[4].url	https://www.sasbdb.org/media/zip_directories/SASDAV7.zip
files[4].path	/data/saxsdb/sasbdb/entries/v7/sasdav7/source/SASDAV7.zip
files[4].size	78974
files[4].sha256	879ff9a2110b787e9951f77ae84ba4e7f8b9c2845adf033591b81702001f72eb
files[4].role	full_entry_zip
files[4].zip_member_count	6
files[4].zip_validation	central_directory_readable

查看完整 summary.json 原文

{
  "code": "SASDAV7",
  "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/SASDAV7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAV7.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV7_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV7_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAV7_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAV7_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAV7.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": "AIR-3A",
          "short_name": null,
          "sequence": "GGGGAGGCUGUGGUGAGGG",
          "organism": null,
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
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查看完整 manifest.json 原文

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Title	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