SASDXH7

GAGE6 60bp dsDNA oligonucleotide

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2026-02-23T09:45:35.560463+01:00

Data was collected at the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus3 S 2M detector at a sample-detector distance of 2.68 m and at a wavelength of λ = 0.107812 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50 μl sample at 2.587 mg/ml was injected onto a GE Superdex 200 5/150 column at 25°C using 150 mM KCl, 20 mM HEPES (pH 7.4), 5 mM MgCl2, 1 mM DTT, 5% glycerol buffer. 400 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. 2sigma errors from the Australian Synchrotron's SAXS/WAXS beamline have been divided by 2 to be compatible with expectations from the ATSAS package This is the 60 bp GAGE6 oligo from Lee et al (2015); Wang et al (2022) which reportedly binds SFPQ. SAXS analysis indicates some degree of curvature which is likely due to the presence of multiple AT repeat regions in the sequence.

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · GAGE6 60bp dsDNA oligonucleotide

Concentration— – — Buffer / pH150 mM KCl, 20 mM HEPES, 5% glycerol, 5 mM MgCl2, 1 mM DTT / 7.5
Experimental temperature— Facility / beamlineAustralian Synchrotron / SAXS/WAXS
Wavelength— nmExposure— s × —

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
GAGE6 60bp dsDNA oligo
View sequence
GCCTTCTGCAAAGAAGTCTTGCGCATCTTTTGTGAAGTTTATTTCTAGCTTTTTGATGCT
DNAHomo sapiens——–—monomerMolecule count 137.101 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1702[3]0.004532581–0.4921416 1/AHas uncertainty columnMissing 0154sasbdb/entries/h7/sasdxh7/source/SASDXH7.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)19.5—Å
i0Guinier0.00486542—arbitrary
i0P(r)0.005087—arbitrary
mwExperimental33.1—kDa
mwPorod63.0—kDa
porod_volumePorod101.0—ų
rgGuinier4.7852.34Å
rgP(r)5.52—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 ATSAS online

χ²: 0.357CorMap p: 0.6005Unit: 1/A

DAMMAVER search envelope which had some curvature used as a search model in DAMMIN

ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—dummyDAMMIN ATSAS onlineP1——Model Image Log
▶

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 name150 mM KCl, 20 mM HEPES, 5% glycerol, 5 mM MgCl2, 1 mM DTTBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2023-03-14Storage / measurement temperature— / —
Exposure time—Frames—
Wavelength—Sample-to-detector distance—
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineAustralian Synchrotron / SAXS/WAXS · Melbourne, Australia
q range0.045 – 4.921Sample 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:156 field values
Field pathRaw value
codeSASDXH7
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titleProbing the statistics of sequence-dependent DNA conformations in solution using SAXS.
project.publication.titleProbing the statistics of sequence-dependent DNA conformations in solution using SAXS.
project.publication.author_listKoning HJ, Pullakhandam A, Whitten AE, Bond CS, Peyrard M
project.publication.journalActa Crystallogr D Struct Biol
project.publication.doi10.1107/S2059798325011556
project.publication.pmid41553140
project.publication.published_date2026 Feb 1
project.statusreleased
project.submitted_date2024-09-18
project.released_date2025-08-12
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experiment.instrument.detector.typeDectris
experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameAustralian Synchrotron
experiment.instrument.cityMelbourne
experiment.instrument.countryAustralia
experiment.instrument.beamline_nameSAXS/WAXS
experiment.instrument.beam_geometryPoint
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourceTrue
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_nameGAGE6 60bp dsDNA oligo
experiment.sample.molecule[0].short_nameGAGE6 oligo
experiment.sample.molecule[0].sequenceGCCTTCTGCAAAGAAGTCTTGCGCATCTTTTGTGAAGTTTATTTCTAGCTTTTTGATGCT
experiment.sample.molecule[0].organismHomo sapiens
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_typeDNA
experiment.sample.molecule[0].uniprot_sequence
experiment.sample.molecule[0].mw37.101
experiment.sample.molecule[0].total_mw37.101
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_description60 bp GAGE6 dsDNA oligonucleotide from the study 'insight into the Tumor Suppression Mechanism from the Structure of Human Polypyrimidine Splicing Factor (PSF/SFPQ) Complexed with a 30mer RNA from Murine Virus-like 30S Transcript‑1' (Wang et al, 2022).
experiment.sample.buffer.name150 mM KCl, 20 mM HEPES, 5% glycerol, 5 mM MgCl2, 1 mM DTT
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.nameGAGE6 60bp dsDNA oligonucleotide
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_nameThe University of Western Australia
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameHeidar
experiment.contributor[0].contributor_surnameKoning
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2023-03-14
experiment.storage_temperaturenull
experiment.cell_temperaturenull
experiment.exposure_timenull
experiment.number_of_framesnull
experiment.wavelengthnull
experiment.sample_detector_distancenull
experiment.concentration_minnull
experiment.concentration_maxnull
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.045
experiment.s_max4.921
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareDAMMIN
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_versionATSAS online
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fits[0].models[0].model_mwnull
fits[0].models[0].bead_radiusnull
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fits[0].models[0].symmetryP1
fits[0].models[0].commentDAMMAVER search area used in DAMMIN
fits[0].models[0].user726
fits[0].fit_unit1/A
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fits[0].softwareDAMMIN
fits[0].chi_square_value0.357
fits[0].p_value0.6005
fits[0].fit_residual_plotSASDXH7_fit1_fitresiduals_img.png
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fits[0].software_versionATSAS online
fits[0].descriptionDAMMAVER search envelope which had some curvature used as a search model in DAMMIN
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionData was collected at the SAXS/WAXS beam line at the Australian Synchrotron (Melbourne, Australia) using a Pilatus3 S 2M detector at a sample-detector distance of 2.68 m and at a wavelength of λ = 0.107812 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50 μl sample at 2.587 mg/ml was injected onto a GE Superdex 200 5/150 column at 25°C using 150 mM KCl, 20 mM HEPES (pH 7.4), 5 mM MgCl2, 1 mM DTT, 5% glycerol buffer. 400 successive 1 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. 2sigma errors from the Australian Synchrotron's SAXS/WAXS beamline have been divided by 2 to be compatible with expectations from the ATSAS package This is the 60 bp GAGE6 oligo from Lee et al (2015); Wang et al (2022) which reportedly binds SFPQ. SAXS analysis indicates some degree of curvature which is likely due to the presence of multiple AT repeat regions in the sequence.
experiment_descriptionnull
tags[]
intensity_unitarbitrary
experimental_mw33.1
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw63.0
porod_mw_errornull
pddf_i00.005087
pddf_i0_errornull
guinier_i00.00486542
guinier_i0_errornull
pddf_rg5.52
pddf_rg_errornull
guinier_rg4.785
guinier_rg_error2.34
pddf_dmax19.5
pddf_dmax_errornull
porod_volume101.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first3
guinier_point_last33
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDXH7_datloglog_img.png
symmetrynull
last_modified2026-02-23T09:45:35.560463+01:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDXH7
statussuccess
started_at2026-08-11T16:27:03.644560+00:00
finished_at2026-08-11T16:27:10.642130+00:00
source_last_modified2026-02-23T09:45:35.560463+01:00
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View the complete summary.json source
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  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
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      "pmid": "41553140",
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  "last_modified": "2026-02-23T09:45:35.560463+01:00",
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}
View the complete manifest.json source
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