SASDGK3

Xrn1 resistance RNA1 from Murray Valley Encephalitis

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).

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Xrn1 resistance RNA1 from Murray Valley Encephalitis

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
Xrn1 resistance RNA-1 from Murray Valley Encephalitis
View sequence
GGAGUCAGGCCAGCCGGUUAGGCUGCCACCGAAGGUUGGUAGACGGUGCUGCCUGCGACCAACCCCAGGAGGACUGGGU
RNAMurray Valley Encephalitis——–—monomerMolecule count 125.7 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1151[3]0.0–0.3 1/AHas uncertainty columnMissing 00sasbdb/entries/k3/sasdgk3/source/SASDGK3.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)8.8—Å
i0Guinier0.02253—arbitrary
i0P(r)0.02278—arbitrary
mwExperimental26.28—kDa
mwPorod19.42—kDa
porod_volumePorod31.07—ų
rgGuinier2.4—Å
rgP(r)2.54—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: 0.094CorMap p: 0.016729Unit: 1/A
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—dummyDAMFILT DAMFILT 5.0 (r7883)———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 date2016-12-09Storage / 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

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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
codeSASDGK3
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.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_nameXrn1 resistance RNA-1 from Murray Valley Encephalitis
experiment.sample.molecule[0].short_nameMVE-xrRNA1
experiment.sample.molecule[0].sequenceGGAGUCAGGCCAGCCGGUUAGGCUGCCACCGAAGGUUGGUAGACGGUGCUGCCUGCGACCAACCCCAGGAGGACUGGGU
experiment.sample.molecule[0].organismMurray Valley Encephalitis
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].mw25.7
experiment.sample.molecule[0].total_mw25.7
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
experiment.sample.buffer.name20mM Tris-HCl, 100mM NaCl, 5mM MgCl2
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameXrn1 resistance RNA1 from Murray Valley Encephalitis
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_nameTsinghua University
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameZhang
experiment.contributor[0].contributor_surnameYikan
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-12-09
experiment.storage_temperature4.0
experiment.cell_temperature25.0
experiment.exposure_time1.0
experiment.number_of_frames30
experiment.wavelength0.08857
experiment.sample_detector_distance2.0
experiment.concentration_min0.75
experiment.concentration_max3.0
experiment.sample_volumenull
experiment.flow_ratenull
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experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].model_titlenull
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estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
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[]
intensity_unitarbitrary
experimental_mw26.28
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
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pddf_dmax_errornull
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porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first3
guinier_point_last27
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDGK3_datloglog_img.png
symmetrynull
last_modified2023-03-02T16:54:16.648202+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDGK3
statussuccess
started_at2026-08-11T14:02:02.731048+00:00
finished_at2026-08-11T14:02:10.516189+00:00
source_last_modified2023-03-02T16:54:16.648202+01:00
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View the complete summary.json source
{
  "code": "SASDGK3",
  "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.",
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      "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"
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View the complete manifest.json source
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