SASDVZ4

ST9a RNA, PKmutant (59 nucleotides in 10 mM MgCl2; dimer)

数据类型:SASBDB 实验数据 状态:Published 曲线类型:SEC-SAS 最后更新:2025-09-01T15:31:28.121164+02:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · ST9a RNA, PKmutant (59 nucleotides in 10 mM MgCl2; dimer)

浓度— – 3.0 缓冲液 / pH50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3 / —
实验温度20.0 设备 / 束线National Synchrotron Light Source II (NSLS-II) / 16-ID (LiX)
波长0.082 nm曝光2.0 s × 1200

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
ST9 PKmutant (59 nt RNA)
查看序列
AAGUACCCUCCAAGCCCUACAGGUUGGAAGAGGGGGCUAUCAGUCCUGAUGGCAGACUC
RNA———–—dimer分子数 219.075 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
1200[3]0.06–10.0 1/nm含误差列缺失 00sasbdb/entries/z4/sasdvz4/source/SASDVZ4.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)12.81—nm
i0Guinier10.2851—arbitrary
i0P(r)10.4—arbitrary
mwExperimental43.7—kDa
porod_volumePorod61.9—nm³
rgGuinier3.520.024nm
rgP(r)3.648—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

该条目没有来源拟合记录。

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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50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3缓冲液浓度—
pH—添加剂—
缓冲液说明10 mM MgCl2 buffer
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2024-01-30储存 / 测量温度20.0 / 20.0
曝光时间2.0帧数1200
波长0.082样品-探测器距离3.561
光源X-ray synchrotron探测器Pilatus3 S 1M
机构 / 束线National Synchrotron Light Source II (NSLS-II) / 16-ID (LiX) · Upton, NY, USA
q 范围0.06 – 10.0样品体积 / 流速95.0 / 0.75

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
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sascifsasbdb/entries/z4/sasdvz4/source/SASDVZ4.sascifnot_available——下载查看原文件源站
summarysasbdb/entries/z4/sasdvz4/source/summary.jsondownloaded619371b2691b255549fdb0b27e2ee9d68b8ea7c199ecf0596ded6507aec2cb02f054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(2 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:134 个字段值
字段路径原始值
codeSASDVZ4
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleA conserved viral RNA fold enables nuclease resistance across kingdoms of life.
project.publication.titleA conserved viral RNA fold enables nuclease resistance across kingdoms of life.
project.publication.author_listGezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL
project.publication.journalNucleic Acids Res
project.publication.doi10.1093/nar/gkaf840
project.publication.pmid40884403
project.publication.published_date2025 Aug 27
project.statusreleased
project.submitted_date2024-07-12
project.released_date2025-07-12
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 S 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameNational Synchrotron Light Source II (NSLS-II)
experiment.instrument.cityUpton, NY
experiment.instrument.countryUSA
experiment.instrument.beamline_name16-ID (LiX)
experiment.instrument.beam_geometrynull
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourceTrue
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_nameST9 PKmutant (59 nt RNA)
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceAAGUACCCUCCAAGCCCUACAGGUUGGAAGAGGGGGCUAUCAGUCCUGAUGGCAGACUC
experiment.sample.molecule[0].organismnull
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeRNA
experiment.sample.molecule[0].uniprot_sequence
experiment.sample.molecule[0].mw19.075
experiment.sample.molecule[0].total_mw38.15
experiment.sample.molecule[0].number_molecules2
experiment.sample.molecule[0].complex_stateFalse
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_description
experiment.sample.buffer.name50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.comment10 mM MgCl2 buffer
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.phnull
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameST9a RNA, PKmutant (59 nucleotides in 10 mM MgCl2; dimer)
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_namenull
experiment.contributor[0].affiliation[0].addressnull
experiment.contributor[0].affiliation[0].full_nameColumbia University Irving Medical Center
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameSophie
experiment.contributor[0].contributor_surnameKorn
experiment.contributor[0].orcidhttps://orcid.org/0000-0003-3798-3277
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2024-01-30
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time2.0
experiment.number_of_frames1200
experiment.wavelength0.082
experiment.sample_detector_distance3.561
experiment.concentration_minnull
experiment.concentration_max3.0
experiment.sample_volume95.0
experiment.flow_rate0.75
experiment.s_min0.06
experiment.s_max10.0
experiment.total_exposure_timenull
experiment.seccolumn1
fits[]
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionnull
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of ST9 RNA, PKmutant (59 nucleotides) in 50 mM Tris pH 7.5, 100 mM NaCl, 1 mM DTT, 10 mM MgCl2, 0.0002% w/v NaN3 were collected on the 16-ID (LiX) beam line at the National Synchrotron Light Source II (NSLS-II; Upton, NY, USA) using a Pilatus3 S 1M detector at a sample-detector distance of 3.6 m and at a wavelength of λ = 0.082 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 95.00 μl sample at 3 mg/ml was injected at a 0.75 ml/min flow rate onto a GE Superdex 200 Increase 10/300 column at 20°C. 1200 successive 2 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.
tags[]
intensity_unitarbitrary
experimental_mw43.7
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i010.4
pddf_i0_errornull
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guinier_i0_errornull
pddf_rg3.648
pddf_rg_errornull
guinier_rg3.52
guinier_rg_error0.024
pddf_dmax12.81
pddf_dmax_errornull
porod_volume61.9
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first8
guinier_point_last31
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDVZ4_datloglog_img.png
symmetrynull
last_modified2025-09-01T15:31:28.121164+02:00
bragg_peak[]
manifest.json:34 个字段值
字段路径原始值
codeSASDVZ4
statussuccess
started_at2026-08-11T16:43:10.885085+00:00
finished_at2026-08-11T16:43:17.387204+00:00
source_last_modified2025-09-01T15:31:28.121164+02:00
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查看完整 summary.json 原文
{
  "code": "SASDVZ4",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "A conserved viral RNA fold enables nuclease resistance across kingdoms of life.",
    "publication": {
      "title": "A conserved viral RNA fold enables nuclease resistance across kingdoms of life.",
      "author_list": "Gezelle JG, Korn SM, McDonald JT, Gong Z, Erickson A, Huang CH, Yang F, Cronin M, Kuo YW, Wimberly BT, Steckelberg AL",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkaf840",
      "pmid": "40884403",
      "published_date": "2025 Aug 27"
    },
    "status": "released",
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  "last_modified": "2025-09-01T15:31:28.121164+02:00",
  "bragg_peak": []
}
查看完整 manifest.json 原文
{
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  "source_last_modified": "2025-09-01T15:31:28.121164+02:00",
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}