SASDG24

Subgenomic flavivirus RNAs from Dengue virus 2

Data type: SASBDB experimental data Status: Published Curve type: Extrapolated to infinite dilution Last updated: 2023-03-02T16:54:16.648202+01:00

The subtracted SAXS data series used to generate the final extrapolated to zero-concentration profile displayed in this entry are provided in the full entry zip archive. The ab initio dummy atom model represents the averaged spatial disposition of the RNA in solution (DAMFILT model), derived from several aligned individual models (corresponding fit).

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Subgenomic flavivirus RNAs from Dengue virus 2

Concentration0.75 – 3.0 Buffer / pH20mM Tris-HCl, 100mM NaCl, 5mM MgCl2 / 7.5
Experimental temperature25.0 Facility / beamlineAdvanced Photon Source (APS), Argonne National Laboratory / 12-ID-B SAXS/WAXS
Wavelength0.08857 nmExposure1.0 s × 30

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Subgenomic flavivirus RNAs from Dengue virus 2
View sequence
GGAGUCAGGUCGGAUUAAGCCAUAGUACGGAAAAAACUAUGCUACCUGUGAGCCCCGUCCAAGGACGUUAAAAGAAGUCAGGCCAUUACAAAUGCCAUAGCUUGAGUAAACUGUGCAGCCUGUAGCUCCACCUGAGAAGGUGUAAAAAAUCUGGGAGGCCACAAACCAUGGAAGCUGUACGCAUGGCGUAGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUACAAAUCGCAGCAACAAUGGGGGCCCAAGGUGAGAUGAAGCUGUAGUCUCACUGGAAGGACUAGAGGUUAGAGGAGACCCCCCCAAAACAAAAAACAGCAUAUUGACGCUGGGAAAGACCAGAGAUCCUGCUGUCUCCUCAGCAUCAUUCCAGGCACAGAACGCCAGAAAAUGGAAUGGUGCUGUUGAAUCAACAGGUUCU
RNADengue virus 2——–—monomerMolecule count 1136.889 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1151[3]0.0–0.3 1/AHas uncertainty columnMissing 00sasbdb/entries/24/sasdg24/source/SASDG24.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)30.5—Å
i0Guinier0.38—arbitrary
i0P(r)0.3931—arbitrary
mwExperimental132.3—kDa
mwPorod147.5—kDa
porod_volumePorod236.0—ų
rgGuinier7.9—Å
rgP(r)8.55—Å

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 · DAMMIN 2.8.3

χ²: 0.53CorMap p: 0.129727Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—dummyDAMFILT 2.8.3———Model Image
▶

4. Source File Index Source Files

▶

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 name20mM Tris-HCl, 100mM NaCl, 5mM MgCl2Buffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-12-16Storage / measurement temperature4.0 / 25.0
Exposure time1.0Frames30
Wavelength0.08857Sample-to-detector distance2.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlineAdvanced Photon Source (APS), Argonne National Laboratory / 12-ID-B SAXS/WAXS · Lemont, IL, USA
q range0.0 – 3.0Sample volume / flow rate— / —

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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All source fields (unfiltered)

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

summary.json:205 field values
Field pathRaw value
codeSASDG24
statusPublished
type_of_curveExtrapolated to infinite dilution
angular_unit1/A
project.titleLong non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution.
project.publication.titleLong non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution.
project.publication.author_listZhang Y, Zhang Y, Liu ZY, Cheng ML, Ma J, Wang Y, Qin CF, Fang X
project.publication.journalEMBO Rep
project.publication.doi10.15252/embr.201847016
project.publication.pmid31502753
project.publication.published_date2019 Nov 5
project.statusreleased
project.submitted_date2019-08-10
project.released_date2019-09-05
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experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.nameAdvanced Photon Source (APS), Argonne National Laboratory
experiment.instrument.cityLemont, IL
experiment.instrument.countryUSA
experiment.instrument.beamline_name12-ID-B SAXS/WAXS
experiment.instrument.beam_geometrynull
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_nameSubgenomic flavivirus RNAs from Dengue virus 2
experiment.sample.molecule[0].short_nameDENV2-sfRNA
experiment.sample.molecule[0].sequenceGGAGUCAGGUCGGAUUAAGCCAUAGUACGGAAAAAACUAUGCUACCUGUGAGCCCCGUCCAAGGACGUUAAAAGAAGUCAGGCCAUUACAAAUGCCAUAGCUUGAGUAAACUGUGCAGCCUGUAGCUCCACCUGAGAAGGUGUAAAAAAUCUGGGAGGCCACAAACCAUGGAAGCUGUACGCAUGGCGUAGUGGACUAGCGGUUAGAGGAGACCCCUCCCUUACAAAUCGCAGCAACAAUGGGGGCCCAAGGUGAGAUGAAGCUGUAGUCUCACUGGAAGGACUAGAGGUUAGAGGAGACCCCCCCAAAACAAAAAACAGCAUAUUGACGCUGGGAAAGACCAGAGAUCCUGCUGUCUCCUCAGCAUCAUUCCAGGCACAGAACGCCAGAAAAUGGAAUGGUGCUGUUGAAUCAACAGGUUCU
experiment.sample.molecule[0].organismDengue virus 2
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_sequencenull
experiment.sample.molecule[0].mw136.889
experiment.sample.molecule[0].total_mw136.889
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_descriptionnull
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experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
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experiment.sample.purity_methodnull
experiment.sample.nameSubgenomic flavivirus RNAs from Dengue virus 2
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
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experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressnull
experiment.contributor[0].affiliation[0].full_nameTsinghua University
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameZhang
experiment.contributor[0].contributor_surnameYikan
experiment.contributor[0].orcid
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experiment.concentration_unitnull
experiment.date2016-12-16
experiment.storage_temperature4.0
experiment.cell_temperature25.0
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pddf_softwareATSAS GNOM
pddf_software_version4.6
i0_calibration_standardnull
descriptionThe subtracted SAXS data series used to generate the final extrapolated to zero-concentration profile displayed in this entry are provided in the full entry zip archive. The ab initio dummy atom model represents the averaged spatial disposition of the RNA in solution (DAMFILT model), derived from several aligned individual models (corresponding fit).
experiment_descriptionnull
tags[]
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experimental_mw132.3
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
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estimated_volumenull
estimated_volume_errornull
guinier_point_first2
guinier_point_last9
pddf_point_firstnull
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i0_calibration_standard_datanull
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symmetrynull
last_modified2023-03-02T16:54:16.648202+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDG24
statussuccess
started_at2026-08-11T14:12:15.028228+00:00
finished_at2026-08-11T14:12:26.925441+00:00
source_last_modified2023-03-02T16:54:16.648202+01:00
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View the complete summary.json source
{
  "code": "SASDG24",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/A",
  "project": {
    "title": "Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution.",
    "publication": {
      "title": "Long non-coding subgenomic flavivirus RNAs have extended 3D structures and are flexible in solution.",
      "author_list": "Zhang Y, Zhang Y, Liu ZY, Cheng ML, Ma J, Wang Y, Qin CF, Fang X",
      "journal": "EMBO Rep",
      "doi": "10.15252/embr.201847016",
      "pmid": "31502753",
      "published_date": "2019 Nov 5"
    },
    "status": "released",
    "submitted_date": "2019-08-10",
    "released_date": "2019-09-05"
  },
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View the complete manifest.json source
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