SASDG92

1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) vesicles: 30 nm filter extrusion

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2024-01-16T15:25:15.619825+01:00

DPPC vesicles were extruded through 30 nm pore-diameter filter prior to analysis. Experimental molecular weight estimates do not apply in this instance (in context of the inherent size-distribution, inter-vesicle interactions and multiple contrasts of the sample) and therefore the MW of one DPPC molecule is quoted. The resulting fit to the data and corresponding plot reflects the relative electron density profile perpendicular to the DPPC bilayer of the vesicles, i.e., a bilayer thickness electron density profile, that takes into account the n-component volume-fraction weighted form factors and size distribution of the DPPC vesicle population in solution. Note: For visualization purposes only, the I(s) axis has been arbitrarily scaled in the primary data display (the downloadable .dat and additional files located in the full-entry zip archive are not scaled accordingly). Before 2024 Jan 16 the downloadable "curve (dat)" was mistakenly sourced from a different dataset although the .dat located under "additional_files" in the full-entry zip archive was correct.

▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) vesicles: 30 nm filter extrusion

Concentration— – 1.0 Buffer / pHwater / 7.0
Experimental temperature45.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure0.05 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
1,2-dipalmitoyl-sn-glycero-3-phosphocholine
View sequence
C40H80NO8P
other———–—monomerMolecule count 10.734 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12625[3]0.0481067–7.28844 1/nmHas uncertainty columnMissing 0180sasbdb/entries/92/sasdg92/source/SASDG92.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)66.0—nm
i0Guinier3546.0—arbitrary
i0P(r)12060.0—arbitrary
mwExperimental1.0—kDa
rgP(r)23.77—nm

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 · Other LIPMIX

χ²: —CorMap p: 0.001Unit: 1/nm
ModelName / TypeSoftwareSymmetryModel MWPDB DeclarationSource file
1—otherOther [static image] ———Model
▶

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 namewaterBuffer concentration—
pH7.0Additives—
Buffer descriptionMilliQ Grade water
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2018-07-09Storage / measurement temperature40.0 / 45.0
Exposure time0.05Frames20
Wavelength0.124Sample-to-detector distance3.1
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.048 – 7.288Sample 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:157 field values
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statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleRestoring structural parameters of lipid mixtures from small-angle X-ray scattering data
project.publication.titleRestoring structural parameters of lipid mixtures from small-angle X-ray scattering data
project.publication.author_listKonarev P, Gruzinov A, Mertens H, Svergun D
project.publication.journalJournal of Applied Crystallography
project.publication.doi10.1107/S1600576720015368
project.publication.pmidnull
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project.statusreleased
project.submitted_date2019-07-17
project.released_date2021-01-27
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descriptionDPPC vesicles were extruded through 30 nm pore-diameter filter prior to analysis. Experimental molecular weight estimates do not apply in this instance (in context of the inherent size-distribution, inter-vesicle interactions and multiple contrasts of the sample) and therefore the MW of one DPPC molecule is quoted. The resulting fit to the data and corresponding plot reflects the relative electron density profile perpendicular to the DPPC bilayer of the vesicles, i.e., a bilayer thickness electron density profile, that takes into account the n-component volume-fraction weighted form factors and size distribution of the DPPC vesicle population in solution. Note: For visualization purposes only, the I(s) axis has been arbitrarily scaled in the primary data display (the downloadable .dat and additional files located in the full-entry zip archive are not scaled accordingly). Before 2024 Jan 16 the downloadable "curve (dat)" was mistakenly sourced from a different dataset although the .dat located under "additional_files" in the full-entry zip archive was correct.
experiment_descriptionSynchrotron SAXS data from solutions of DPCC vesicles in water, pH 7 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10 mg/ml was measured at 45°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.
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statussuccess
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View the complete summary.json source
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      "description": ""
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  "description": "DPPC vesicles were extruded through 30 nm pore-diameter filter prior to analysis. Experimental molecular weight estimates do not apply in this instance (in context of the inherent size-distribution, inter-vesicle interactions and multiple contrasts of the sample) and therefore the MW of one DPPC molecule is quoted. The resulting fit to the data and corresponding plot reflects the relative electron density profile perpendicular to the DPPC bilayer of the vesicles, i.e., a bilayer thickness electron density profile, that takes into account the n-component volume-fraction weighted form factors and size distribution of the DPPC vesicle population in solution. Note: For visualization purposes only, the I(s) axis has been arbitrarily scaled in the primary data display (the downloadable .dat and additional files located in the full-entry zip archive are not scaled accordingly). Before 2024 Jan 16 the downloadable \"curve (dat)\" was mistakenly sourced from a different dataset although the .dat located under \"additional_files\" in the full-entry zip archive was correct.",
  "experiment_description": "Synchrotron SAXS data from solutions of DPCC vesicles in water, pH 7 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3.1 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10 mg/ml was measured at 45°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.",
  "tags": [
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    "softmatter"
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  "guinier_rg_error": null,
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  "pddf_point_first": null,
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  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDG92_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2024-01-16T15:25:15.619825+01:00",
  "bragg_peak": []
}
View the complete manifest.json source
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