SASDGF3

Xrn1 resistance RNA1 from Zika virus

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 · Xrn1 resistance RNA1 from Zika virus

Concentration0.25 – 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 nmExposure0.5 s × 30

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Xrn1 resistance RNA2 from Zika virus
View sequence
AGUCAGGCCGAGAACGCCAUGGCACGGAAGAAGCCAUGCUGCCUGUGAGCCCCUCAGAGGACACUGAG
RNAZika virus——–—monomerMolecule count 122.091 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1151[3]0.0–0.3 1/AHas uncertainty columnMissing 00sasbdb/entries/f3/sasdgf3/source/SASDGF3.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)8.50.2Å
i0Guinier0.086720.00043arbitrary
i0P(r)0.086940.00031arbitrary
mwExperimental22.14—kDa
mwPorod21.15—kDa
porod_volumePorod33.84—ų
rgGuinier2.430.02Å
rgP(r)2.50.01Å

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

▼

3. Source Fits and Models Source Fits & Models

Fit 2 · DAMMIN 2.8.3

χ²: 0.495CorMap p: 0.0Unit: 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 date2016-12-09Storage / measurement temperature4.0 / 25.0
Exposure time0.5Frames30
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:182 field values
Field pathRaw value
codeSASDGF3
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.countryUSA
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experiment.sample.molecule[0].short_nameZIKV-xrRNA2
experiment.sample.molecule[0].sequenceAGUCAGGCCGAGAACGCCAUGGCACGGAAGAAGCCAUGCUGCCUGUGAGCCCCUCAGAGGACACUGAG
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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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intensities_log_log_plotSASDGF3_datloglog_img.png
symmetrynull
last_modified2023-03-02T16:54:16.648202+01:00
bragg_peak[]
manifest.json:36 field values
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codeSASDGF3
statussuccess
started_at2026-08-11T13:59:03.148530+00:00
finished_at2026-08-11T13:59:13.739115+00:00
source_last_modified2023-03-02T16:54:16.648202+01:00
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View the complete summary.json source
{
  "code": "SASDGF3",
  "status": "Published",
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  "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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