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SASDX49

Group IIC intron Domain 1, 2 & 3

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2025-11-28T16:19:39.330229+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Group IIC intron Domain 1, 2 & 3

Concentration— – 1.13 Buffer / pH10 mM MgCl2, 5 mM Na-MES / 6.5
Experimental temperature25.0 Facility / beamlineESRF / BM29
Wavelength0.9918 nmExposure2.0 s × 1700

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Group IIC Intron Domain 1, 2 & 3
View sequence
GGGUUAUGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAA
RNAOceanobacillus iheyensis——–—monomerMolecule count 1103.0 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1982[3]0.137017–5.205441 1/nmHas uncertainty columnMissing 041sasbdb/entries/49/sasdx49/source/SASDX49.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)12.04—nm
i0Guinier21.4185—1/cm
i0P(r)21.66—1/cm
mwExperimental92.3—kDa
mwGuinier I(0)92.3—kDa
porod_volumePorod195.2—nm³
rgGuinier3.590.04nm
rgP(r)3.675—nm

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

▼

3. Source Fits and Models Source Fits & Models

Fit 1 · DAMMIF

χ²: 0.96CorMap p: 0.7952Unit: 1/A

Fit data Fit plot Residual plot

ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—dummyDAMMIF dammif (r13469)———Model Image
▶

4. Source File Index Source Files

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5. Experiment Description and Publication Experiment & Publication

▼

6. Complete Source Record Complete Source Record

The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.

Open the original SASBDB entry

Buffer and Sample Properties

Buffer name10 mM MgCl2, 5 mM Na-MESBuffer concentration—
pH6.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2021-09-02Storage / measurement temperature25.0 / 25.0
Exposure time2.0Frames1700
Wavelength0.9918Sample-to-detector distance2.827
SourceX-ray synchrotronDetectorPilatus3 2M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.137 – 5.205Sample volume / flow rate95.0 / 0.5

Original SASBDB Plots

Experimental I(q)
Experimental I(q)
Experimental I(q), log-log
Experimental I(q), log-log
Guinier plot
Guinier plot
Kratky plot
Kratky plot
P(r) plot
P(r) plot

Downloadable Files

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sascifsasbdb/entries/49/sasdx49/source/SASDX49.sascifnot_available——DownloadView source fileSource site
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full_entry_zip：source record and ZIP contents (4 items)
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pddf：source record
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sascif：source record
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summary：source record
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All source fields (unfiltered)

Every source field is expanded here, including empty values, list members and fields already shown above.

summary.json：156 field values
Field pathRaw value
codeSASDX49
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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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, 2 & 3
experiment.sample.molecule[0].short_nameD1-3
experiment.sample.molecule[0].sequenceGGGUUAUGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAA
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].mw103.0
experiment.sample.molecule[0].total_mw103.0
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, 2 & 3
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.date2021-09-02
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_min0.137
experiment.s_max5.205
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].chi_square_value0.96
fits[0].p_value0.7952
fits[0].fit_residual_plotSASDX49_fit1_fitresiduals_img.png
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fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionnull
tags[]
intensity_unit1/cm
experimental_mw92.3
experimental_mw_errornull
guinier_i0_mw92.3
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i021.66
pddf_i0_errornull
guinier_i021.4185
guinier_i0_errornull
pddf_rg3.675
pddf_rg_errornull
guinier_rg3.59
guinier_rg_error0.04
pddf_dmax12.04
pddf_dmax_errornull
porod_volume195.2
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first5
guinier_point_last44
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDX49_datloglog_img.png
symmetrynull
last_modified2025-11-28T16:19:39.330229+01:00
bragg_peak[]
manifest.json：34 field values
Field pathRaw value
codeSASDX49
statussuccess
started_at2026-08-11T16:38:37.080081+00:00
finished_at2026-08-11T16:38:44.564586+00:00
source_last_modified2025-11-28T16:19:39.330229+01:00
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View the complete summary.json source
{
  "code": "SASDX49",
  "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"
  },
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          "short_name": "D1-3",
          "sequence": "GGGUUAUGUGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUAACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCAAACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGCAUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGAAGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAGUACCCUGUUCGCAGGGGAAGGACGGAA",
          "organism": "Oceanobacillus iheyensis",
          "uniprot_code": null,
          "uniprot_range_first": null,
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          "molecule_description": ""
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View the complete manifest.json source
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