SASDCE5

Light encoded DNA biosensor: e13A DNA

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2019-12-06T13:07:15.624532+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Light encoded DNA biosensor: e13A DNA

Concentration0.25 – 2.0 Buffer / pH154 mM NaCl / 8.3
Experimental temperature5.0 Facility / beamlineESRF / BM29
Wavelength0.1 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
e13A
View sequence
CCACGCCAAACGCTGAAGGGCTTCTTCCTTATTTTTGGCGTGGCCACGCCAAACG
DNA———–—monomerMolecule count 116.903 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1976[3]0.290952–4.49359 1/nmHas uncertainty columnMissing 06sasbdb/entries/e5/sasdce5/source/SASDCE5.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)8.00.5nm
i0Guinier32.03.0—
i0P(r)32.03.0—
mwExperimental15.0—kDa
mwGuinier I(0)14.02.0kDa
mwPorod17.0—kDa
porod_volumePorod24.0—nm³
rgGuinier2.320.03nm
rgP(r)2.360.04nm

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

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3. Source Fits and Models Source Fits & Models

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4. Source File Index Source Files

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5. Experiment Description and Publication Experiment & Publication

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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 name154 mM NaClBuffer concentration—
pH8.3Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2013-11-22Storage / measurement temperature5.0 / 5.0
Exposure time0.05Frames20
Wavelength0.1Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.291 – 4.494Sample 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
codeSASDCE5
statusPublished
type_of_curveMerged
angular_unit1/nm
project.titleOptical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor.
project.publication.titleOptical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor.
project.publication.author_listCordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV
project.publication.journalACS Chem Biol
project.publication.doi10.1021/acschembio.8b00029
project.publication.pmid29562136
project.publication.published_date2018 May 18
project.statusreleased
project.submitted_date2017-06-23
project.released_date2018-04-03
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experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
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experiment.sample.molecule[0].long_namee13A
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceccacgccaaacgctgaagggcttcttccttatttttggcgtggccacgccaaacg
experiment.sample.molecule[0].organismnull
experiment.sample.molecule[0].uniprot_codenull
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experiment.sample.molecule[0].molecular_typeDNA
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experiment.contributor[0].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_namePetr
experiment.contributor[0].contributor_surnameKonarev
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
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experiment.storage_temperature5.0
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experiment_descriptionSynchrotron SAXS data from solutions of Light encoded DNA biosensor: e13A DNA in 154 mM NaCl, pH 8.3 were collected at the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2 mg/ml were measured at 5°C. 20 successive 0.050 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 and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve. The model depicts the averaged spatial representation of the DNA (DAMFILT occupancy and volume-corrected bead model).
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last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
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statussuccess
started_at2026-08-11T14:46:14.699633+00:00
finished_at2026-08-11T14:46:22.913091+00:00
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View the complete summary.json source
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  "status": "Published",
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  "angular_unit": "1/nm",
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    "title": "Optical and Structural Characterization of a Chronic Myeloid Leukemia DNA Biosensor.",
    "publication": {
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      "author_list": "Cordeiro M, Otrelo-Cardoso AR, Svergun DI, Konarev PV, Lima JC, Santos-Silva T, Baptista PV",
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  "experiment_description": "Synchrotron SAXS data from solutions of Light encoded DNA biosensor: e13A DNA in 154 mM NaCl, pH 8.3 were collected at the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.3 and 2 mg/ml were measured at 5°C. 20 successive 0.050 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 and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve. The model depicts the averaged spatial representation of the DNA (DAMFILT occupancy and volume-corrected bead model).",
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  "pddf_point_first": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDCE5_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}
View the complete manifest.json source
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