SASDCT7

PYR16(4.6)SN-f5

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

Sample 1 · PYR16(4.6)SN-f5

Concentration0.95 – 7.6 Buffer / pH20 mM Tris 150 mM NaCl 10% glycerol / 7.5
Experimental temperature20.0 Facility / beamlineESRF / BM29
Wavelength0.1 nmExposure1.0 s × 10

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
PYR16(4.6)SN-f5
View sequence
MLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDENSQLEEKISQLKQKNSELKEEIQQLEYGSGPGSPEDEIRQLEQENSQLERENQRLEQEIYQLERGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDEIQQLEEKNSQLKQEISQLEEKNQELKYGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGSPEDKNSELKEEIQQLEEENQQLEEKISELKYGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKGSGPGSPEDEIQQLEEEISQLEQKNSELKEKNQELKYGSGPGSPEDKISELKEENQQLEQKIQQLKEENSQLEYGSGPGSPEDENQSLEQKNSQLKQEISQLEQEIQQLEYGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKGSGPGSPEDKIEELKEKNSQLKEKNEELKQKIYELKEGSGPGSPEDKNSQLKEENSQLEEKIEQLKEKIQELKYGSGPGSPEDKISQLKEKIQQLKQENQQLEEENSQLEYGLEHHHHHHHH
proteinsynthetic construct——–—monomerMolecule count 171.652 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11008[3]0.197856–4.94475 1/nmHas uncertainty columnMissing 00sasbdb/entries/t7/sasdct7/source/SASDCT7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)11.31.0nm
i0Guinier65.350.05—
i0P(r)65.230.05—
mwExperimental65.4—kDa
mwGuinier I(0)65.40.5kDa
mwPorod80.0—kDa
porod_volumePorod136.0—nm³
rgGuinier3.830.01nm
rgP(r)3.8120.003nm

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 name20 mM Tris 150 mM NaCl 10% glycerolBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2016-02-16Storage / measurement temperature20.0 / 20.0
Exposure time1.0Frames10
Wavelength0.1Sample-to-detector distance2.89
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.198 – 4.945Sample 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
codeSASDCT7
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleDesign of coiled-coil protein-origami cages that self-assemble in vitro and in vivo.
project.publication.titleDesign of coiled-coil protein-origami cages that self-assemble in vitro and in vivo.
project.publication.author_listLjubetič A, Lapenta F, Gradišar H, Drobnak I, Aupič J, Strmšek Ž, Lainšček D, Hafner-Bratkovič I, Majerle A, Krivec N, Benčina M, Pisanski T, Veličković TĆ, Round A, Carazo JM, Melero R, Jerala R
project.publication.journalNat Biotechnol
project.publication.doi10.1038/nbt.3994
project.publication.pmid29035374
project.publication.published_date2017 Nov
project.statusreleased
project.submitted_date2017-09-28
project.released_date2017-10-09
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experiment.instrument.detector.namePilatus 1M
experiment.instrument.detector.resolution172.0
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
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experiment.instrument.sample_path_lengthnull
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experiment.instrument.line_collimation_integrationwidthnull
experiment.instrument.xray_energynull
experiment.instrument.beam_profile_ahnull
experiment.instrument.beam_profile_alnull
experiment.sample.molecule[0].long_namePYR16(4.6)SN-f5
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDENSQLEEKISQLKQKNSELKEEIQQLEYGSGPGSPEDEIRQLEQENSQLERENQRLEQEIYQLERGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDEIQQLEEKNSQLKQEISQLEEKNQELKYGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGSPEDKNSELKEEIQQLEEENQQLEEKISELKYGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKGSGPGSPEDEIQQLEEEISQLEQKNSELKEKNQELKYGSGPGSPEDKISELKEENQQLEQKIQQLKEENSQLEYGSGPGSPEDENQSLEQKNSQLKQEISQLEQEIQQLEYGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKGSGPGSPEDKIEELKEKNSQLKEKNEELKQKIYELKEGSGPGSPEDKNSQLKEENSQLEEKIEQLKEKIQELKYGSGPGSPEDKISQLKEKIQQLKQENQQLEEENSQLEYGLEHHHHHHHH
experiment.sample.molecule[0].organismsynthetic construct
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_typeprotein
experiment.sample.molecule[0].uniprot_sequencenull
experiment.sample.molecule[0].mw71.652
experiment.sample.molecule[0].total_mw71.652
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.name20 mM Tris 150 mM NaCl 10% glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
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experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.namePYR16(4.6)SN-f5
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_nameNational Research Council
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameJana
experiment.contributor[0].contributor_surnameAupič
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2016-02-16
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experiment.cell_temperature20.0
experiment.exposure_time1.0
experiment.number_of_frames10
experiment.wavelength0.1
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experiment.flow_ratenull
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fits[0].models[0].pdb_link[]
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fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of PYR16SN in 20 mM Tris, 150 mM NaCl, 10% glycerol, pH 7.5, were collected at the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.89 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, where 2θ is the scattering angle). A solute concentration series ranging between 1 and 7.6 mg/ml were measured at 20°C. For each sample, data was collected over 10 frames lasting 1 s. The data were normalized to the intensity of the transmitted beam and radially averaged. Each individual frames were carefully inspected for radiation damage and those not showing any radiation damage were then averaged. The scattering of the matched solvent-blank was subtracted and the different curves were scaled for protein concentration. Scattering curves were analyzed using PRIMUS software.
tags[]
intensity_unitnull
experimental_mw65.4
experimental_mw_errornull
guinier_i0_mw65.4
guinier_i0_mw_error0.5
porod_mw80.0
porod_mw_errornull
pddf_i065.23
pddf_i0_error0.05
guinier_i065.35
guinier_i0_error0.05
pddf_rg3.812
pddf_rg_error0.003
guinier_rg3.83
guinier_rg_error0.01
pddf_dmax11.3
pddf_dmax_error1.0
porod_volume136.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last30
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCT7_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCT7
statussuccess
started_at2026-08-11T16:32:48.658448+00:00
finished_at2026-08-11T16:32:57.983523+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
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View the complete summary.json source
{
  "code": "SASDCT7",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo.",
    "publication": {
      "title": "Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo.",
      "author_list": "Ljubetič A, Lapenta F, Gradišar H, Drobnak I, Aupič J, Strmšek Ž, Lainšček D, Hafner-Bratkovič I, Majerle A, Krivec N, Benčina M, Pisanski T, Veličković TĆ, Round A, Carazo JM, Melero R, Jerala R",
      "journal": "Nat Biotechnol",
      "doi": "10.1038/nbt.3994",
      "pmid": "29035374",
      "published_date": "2017 Nov"
    },
    "status": "released",
    "submitted_date": "2017-09-28",
    "released_date": "2017-10-09"
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    "sample": {
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          "long_name": "PYR16(4.6)SN-f5",
          "short_name": null,
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          "molecular_type": "protein",
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