SASDX39

Group IIC Intron Domain 1

数据类型:SASBDB 实验数据 状态:Published 曲线类型:SEC-SAS 最后更新:2025-11-28T16:19:38.013155+01:00
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1. 样品、组分与实验条件 Sample & Experiment

样品 1 · Group IIC Intron Domain 1

浓度— – 1.13 缓冲液 / pH10 mM MgCl2, 5 mM Na-MES / 6.5
实验温度25.0 设备 / 束线ESRF / BM29
波长0.9918 nm曝光2.0 s × 1700

分子组分

组分类型 / 物种UniProt 与构建体寡聚状态分子量
Group IIC Intron Domain 1
查看序列
GGGUUAUGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGG
RNAOceanobacillus iheyensis——–—monomer分子数 189.0 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
11000[3]0.04401839–5.205441 1/nm含误差列缺失 0225sasbdb/entries/39/sasdx39/source/SASDX39.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)12.98—nm
i0Guinier23.6779—1/cm
i0P(r)23.69—1/cm
mwExperimental113.1—kDa
porod_volumePorod187.58—nm³
rgGuinier3.7970.201nm
rgP(r)3.765—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 · DAMMIF

χ²:1.072CorMap p:0.1738单位:1/A
模型名称 / 类型软件对称性模型 MWPDB 声明来源文件
1—dummyDAMMIF dammif (r12736)———模型 图片
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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10 mM MgCl2, 5 mM Na-MES缓冲液浓度—
pH6.5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2021-07-07储存 / 测量温度25.0 / 25.0
曝光时间2.0帧数1700
波长0.9918样品-探测器距离2.827
光源X-ray synchrotron探测器Pilatus3 2M
机构 / 束线ESRF / BM29 · Grenoble, France
q 范围0.044 – 5.205样品体积 / 流速95.0 / 0.5

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
curvesasbdb/entries/39/sasdx39/source/SASDX39.datdownloaded472203fc70864efc9002813d7cfe0dbc3fe5e5cc502df78d3256907492261babe99af下载查看原文件源站
full_entry_zipsasbdb/entries/39/sasdx39/source/SASDX39.zipdownloaded11064568410b5b9197634e4b5e89a1b966a99b7bb6cee37db42029a1ad26526e49ddd0下载查看原文件源站
pddfsasbdb/entries/39/sasdx39/source/SASDX39.outdownloaded40823a2371ea921e7ac918942a0e0f7067d1d87b88afa755837a364067e4d107229c5下载查看原文件源站
sascifsasbdb/entries/39/sasdx39/source/SASDX39.sascifnot_available——下载查看原文件源站
summarysasbdb/entries/39/sasdx39/source/summary.jsondownloaded646078b5c86c8b8c108ed920dbba61b28ba5c72df5fef83d3a67dc349fb0372d15d5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(4 项)
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pddf:来源记录
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sascif:来源记录
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  "role": "sascif",
  "status": "not_available",
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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:156 个字段值
字段路径原始值
codeSASDX39
statusPublished
type_of_curveSEC-SAS
angular_unit1/nm
project.titleDynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.
project.publication.titleDynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.
project.publication.author_listJadhav S, Maiorca M, Manigrasso J, Saha S, Rakitch A, Muscat S, Mulvaney T, De Vivo M, Topf M, Marcia M
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-025-65502-8
project.publication.pmid41309593
project.publication.published_date2025 Nov 27
project.statusreleased
project.submitted_date2025-09-15
project.released_date2025-10-26
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intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDX39.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX39_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX39_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX39_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDX39_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDX39.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 2M
experiment.instrument.detector.resolution0.172
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometrypoint
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_nameGroup IIC Intron Domain 1
experiment.sample.molecule[0].short_nameD1
experiment.sample.molecule[0].sequenceGGGUUAUGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGG
experiment.sample.molecule[0].organismOceanobacillus iheyensis
experiment.sample.molecule[0].uniprot_codenull
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeRNA
experiment.sample.molecule[0].uniprot_sequence
experiment.sample.molecule[0].mw89.0
experiment.sample.molecule[0].total_mw89.0
experiment.sample.molecule[0].number_molecules1
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.name10 mM MgCl2, 5 mM Na-MES
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph6.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameGroup IIC Intron Domain 1
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_nameUppsala University
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameShekhar
experiment.contributor[0].contributor_surnameJadhav
experiment.contributor[0].orcidhttps://orcid.org/0009-0009-4682-7568
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2021-07-07
experiment.storage_temperature25.0
experiment.cell_temperature25.0
experiment.exposure_time2.0
experiment.number_of_frames1700
experiment.wavelength0.9918
experiment.sample_detector_distance2.827
experiment.concentration_minnull
experiment.concentration_max1.13
experiment.sample_volume95.0
experiment.flow_rate0.5
experiment.s_min0.044
experiment.s_max5.205
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDX39_fit1_model1_img.png
fits[0].models[0].softwareDAMMIF
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_versiondammif (r12736)
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDX39_fit1_model1.pdb
fits[0].models[0].model_mwnull
fits[0].models[0].bead_radius2.0
fits[0].models[0].lognull
fits[0].models[0].symmetrynull
fits[0].models[0].commentnull
fits[0].models[0].user1274
fits[0].fit_unit1/A
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fits[0].softwareDAMMIF
fits[0].chi_square_value1.072
fits[0].p_value0.1738
fits[0].fit_residual_plotSASDX39_fit1_fitresiduals_img.png
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fits[0].fit_lognull
fits[0].software_versionnull
fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unit1/cm
experimental_mw113.1
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i023.69
pddf_i0_errornull
guinier_i023.6779
guinier_i0_errornull
pddf_rg3.765
pddf_rg_errornull
guinier_rg3.797
guinier_rg_error0.201
pddf_dmax12.98
pddf_dmax_errornull
porod_volume187.58
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first16
guinier_point_last36
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDX39_datloglog_img.png
symmetrynull
last_modified2025-11-28T16:19:38.013155+01:00
bragg_peak[]
manifest.json:34 个字段值
字段路径原始值
codeSASDX39
statussuccess
started_at2026-08-11T16:28:20.906615+00:00
finished_at2026-08-11T16:28:30.015655+00:00
source_last_modified2025-11-28T16:19:38.013155+01:00
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files[1].rolecurve
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files[3].statusnot_available
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files[4].zip_validationcentral_directory_readable
查看完整 summary.json 原文
{
  "code": "SASDX39",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.",
    "publication": {
      "title": "Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.",
      "author_list": "Jadhav S, Maiorca M, Manigrasso J, Saha S, Rakitch A, Muscat S, Mulvaney T, De Vivo M, Topf M, Marcia M",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-025-65502-8",
      "pmid": "41309593",
      "published_date": "2025 Nov 27"
    },
    "status": "released",
    "submitted_date": "2025-09-15",
    "released_date": "2025-10-26"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDX39.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDX39.dat",
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDX39_pofr_img.png",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDX39.sascif",
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        "name": "Pilatus3 2M",
        "resolution": 0.172
      },
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      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "point",
      "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
    },
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          "long_name": "Group IIC Intron Domain 1",
          "short_name": "D1",
          "sequence": "GGGUUAUGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGG",
          "organism": "Oceanobacillus iheyensis",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "RNA",
          "uniprot_sequence": "",
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          "total_mw": 89.0,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": ""
        }
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        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
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        "ph": 6.5,
        "deuteration": null
      },
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      "name": "Group IIC Intron Domain 1",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
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            "address": null,
            "full_name": "Uppsala University",
            "webpage": null
          }
        ],
        "contributor_name": "Shekhar",
        "contributor_surname": "Jadhav",
        "orcid": "https://orcid.org/0009-0009-4682-7568"
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    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2021-07-07",
    "storage_temperature": 25.0,
    "cell_temperature": 25.0,
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    "s_max": 5.205,
    "total_exposure_time": null,
    "seccolumn": null
  },
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}
查看完整 manifest.json 原文
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