SASDCU7

TRIP18(7.5R)SN-f5

Data type: SASBDB experimental data Status: Published Curve type: Merged Last updated: 2023-06-21T07:56:18.120449+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · TRIP18(7.5R)SN-f5

Concentration0.4 – 4.1 Buffer / pH20 mM Tris 150 mM NaCl 10% glycerol / 7.5
Experimental temperature20.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure0.045 s × 20

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
TRIP18(7.5R)SN-f5
View sequence
MSPEDENSQLEEKISQLKQKNSELKEEIQQLEYGSGPGLEQIEERLEQIEERLQAKEWEKAQLREELQALREKLAQLGSGPGSPEDEIRQLEQENSQLERENQRLEQEIYQLERGSGPGSPEDKNSELKEEIQQLEEENQQLEEKISELKYGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDENQSLEQKNSQLKQEISQLEQEIQQLEYGSGPGLEQIEERLEQIEERLQAKEWEKAQLREELQALREKLAQLGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGSPEDEIQQLEEEISQLEQKNSELKEKNQELKYGSGPGSPEDENQSLEQEISQLEQEIQQLEQKNSELKYGSGPGSPEDKNSQLKEENSQLEEKIEQLKEKIQELKYGSGPGSPEDKIEELKEKNSQLKEKNEELKQKIYELKEGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKGSGPGSPEDKNEQLKEKISELKEKIEQLKEENQSLEYGSGPGLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDKISQLKEKIQQLKQENQQLEEENSQLEYGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKLEHHHHHHHH
proteinsynthetic construct——–—monomerMolecule count 181.866 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11207[3]0.1435935–6.715565 1/nmHas uncertainty columnMissing 04sasbdb/entries/u7/sasdcu7/source/SASDCU7.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)14.512.0nm
i0Guinier12523.6131.0—
i0P(r)12430.040.0—
mwExperimental92.0—kDa
mwGuinier I(0)92.01.0kDa
mwPorod123.0—kDa
porod_volumePorod210.0—nm³
rgGuinier4.230.1nm
rgP(r)4.190.02nm

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 date2016-06-10Storage / measurement temperature10.0 / 20.0
Exposure time0.045Frames20
Wavelength0.124Sample-to-detector distance2.0
SourceX-ray synchrotronDetectorPilatus 1M-W
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.144 – 6.716Sample 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:169 field values
Field pathRaw value
codeSASDCU7
statusPublished
type_of_curveMerged
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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sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDCU7.sascif
experiment.instrument.detector.typeCustom-built
experiment.instrument.detector.namePilatus 1M-W
experiment.instrument.detector.resolution0.172
experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
experiment.instrument.beam_geometryPoint
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
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_nameTRIP18(7.5R)SN-f5
experiment.sample.molecule[0].short_nameTRIP18SN
experiment.sample.molecule[0].sequenceMSPEDENSQLEEKISQLKQKNSELKEEIQQLEYGSGPGLEQIEERLEQIEERLQAKEWEKAQLREELQALREKLAQLGSGPGSPEDEIRQLEQENSQLERENQRLEQEIYQLERGSGPGSPEDKNSELKEEIQQLEEENQQLEEKISELKYGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDENQSLEQKNSQLKQEISQLEQEIQQLEYGSGPGLEQIEERLEQIEERLQAKEWEKAQLREELQALREKLAQLGSGPGSRMKQLEDKVEELLSKNYHLENEVERLKKLVGSGPGSPEDEIQQLEEEISQLEQKNSELKEKNQELKYGSGPGSPEDENQSLEQEISQLEQEIQQLEQKNSELKYGSGPGSPEDKNSQLKEENSQLEEKIEQLKEKIQELKYGSGPGSPEDKIEELKEKNSQLKEKNEELKQKIYELKEGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKGSGPGSPEDKNEQLKEKISELKEKIEQLKEENQSLEYGSGPGLEEELKQLEEELQAIEEQLAQLQWKAQARKEKLAQLKEKLGSGPGSPEDKISQLKEKIQQLKQENQQLEEENSQLEYGSGPGDIEQELERAKESIRRLEQEVNQERSRMQYLQTLLEKLEHHHHHHHH
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].mw81.866
experiment.sample.molecule[0].total_mw81.866
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
experiment.sample.buffer.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameTRIP18(7.5R)SN-f5
experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
experiment.sample.specific_volnull
experiment.sample.dry_volnull
experiment.sample.absorbptionnull
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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.date2016-06-10
experiment.storage_temperature10.0
experiment.cell_temperature20.0
experiment.exposure_time0.045
experiment.number_of_frames20
experiment.wavelength0.124
experiment.sample_detector_distance2.0
experiment.concentration_min0.4
experiment.concentration_max4.1
experiment.sample_volumenull
experiment.flow_ratenull
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experiment.s_max6.716
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].softwareMODELLER
fits[0].models[0].pdb_link[]
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fits[0].models[0].bead_radius1.9
fits[0].models[0].lognull
fits[0].models[0].symmetry
fits[0].models[0].commentThe model contributes 76% to the observed scattering curve.
fits[0].models[0].user201
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fits[0].models[1].bead_radius1.9
fits[0].models[1].lognull
fits[0].models[1].symmetry
fits[0].models[1].commentThe model contributes 24% to the observed scattering curve.
fits[0].models[1].user201
fits[0].fit_unit1/A
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fits[0].softwareOLIGOMER
fits[0].chi_square_value0.96
fits[0].p_value0.0
fits[0].fit_residual_plotSASDCU7_fit1_fitresiduals_img.png
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fits[0].software_version2.7.2
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of TRIP18(7.5R)SN-f5 in 20 mM Tris 150 mM NaCl 10% glycerol, pH 7.5 were collected on the P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 1M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.124 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.4 and 4.1 mg/ml were measured at 20°C. 20 successive 0.045 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. To detect any potential concentration dependent effects a series consisting of 3 concentrations was measured. The highest concentration was 4.1 mg/ml, while the lowest concentrations was 0.4 mg/ml. Frames were carefully inspected for radiation damage and those not showing any radiation damage were then averaged. Before and after each sample scattering, matching buffer was measured and subtracted from sample scattering. Scattering curves were merged and analyzed using PRIMUS software.
tags[]
intensity_unitnull
experimental_mw92.0
experimental_mw_errornull
guinier_i0_mw92.0
guinier_i0_mw_error1.0
porod_mw123.0
porod_mw_errornull
pddf_i012430.0
pddf_i0_error40.0
guinier_i012523.6
guinier_i0_error131.0
pddf_rg4.19
pddf_rg_error0.02
guinier_rg4.23
guinier_rg_error0.1
pddf_dmax14.51
pddf_dmax_error2.0
porod_volume210.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first1
guinier_point_last15
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDCU7_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:18.120449+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDCU7
statussuccess
started_at2026-08-11T16:37:57.360208+00:00
finished_at2026-08-11T16:38:06.660261+00:00
source_last_modified2023-06-21T07:56:18.120449+02:00
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View the complete summary.json source
{
  "code": "SASDCU7",
  "status": "Published",
  "type_of_curve": "Merged",
  "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"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCU7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCU7.dat",
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  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCU7_kratky_img.png",
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      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": "Point",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
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      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "TRIP18(7.5R)SN-f5",
          "short_name": "TRIP18SN",
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            "address": null,
            "full_name": "National Research Council",
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  "last_modified": "2023-06-21T07:56:18.120449+02:00",
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View the complete manifest.json source
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