SASDE89

Interleukin-1 receptor accessory protein ectodomain with RII linker

Data type: SASBDB experimental data Status: Published Curve type: SEC-SAS Last updated: 2020-11-27T12:00:32.590807+01:00

SEC-SAXS was performed at 20°C using the following parameters: Column: Schodex kw-803 ; Flow rate: 0.5 mL/min; Total acquisition time: 30min; Sample injection concentration: 7.8 mg/mL; Injection volume: 50 μL.

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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Interleukin-1 receptor accessory protein ectodomain with RII linker

Concentration— – 7.8 Buffer / pH10mM HEPES, 150mM NaCl, 3% glycerol / 7.2
Experimental temperature20.0 Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS)
Wavelength0.103 nmExposure3.0 s × 600

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Interleukin-1 receptor accessory protein ectodomains with RII linker
View sequence
SERCDDWGLDTMRQIQVFEDEPARIKCPLFEHFLKFNYSTAHSAGLTLIWYWTRQDRDLEEPINFRLPENRISKEKDVLWFRPTLLNDTGNYTCMLRNTTYCSKVAFPLEVVQKDSCFNSPMKLPVHKLYIEYGIQRITCPNVDGYFPSSVKPTITWYMGCYKIQNFNNVIPEGMNLSFLIALISNNGNYTCVVTYPENGRTFHLTRTLTVKVKKKKEETIPVIHSPNDHVVYEKEPGEELLIPCTVYFSFLMDSRNEVWWTIDGKKPDDITIDVTINESISHSRTEDETRTQILSIKKVTSEDLKRSYVCHARSAKGEVAKAAKVKAAALHHILDAQKMVWNHRHHHHHH
proteinHomo sapiensQ9NPH321–348monomerMolecule count 140.893 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
1984[3]0.0131–0.560837 1/AHas uncertainty columnMissing 032sasbdb/entries/89/sasde89/source/SASDE89.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.66—Å
i0Guinier342.70.9arbitrary
i0P(r)345.1—arbitrary
mwExperimental50.2—kDa
porod_volumePorod75.0—ų
rgGuinier3.0430.1Å
rgP(r)3.12—Å

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

▶

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 name10mM HEPES, 150mM NaCl, 3% glycerolBuffer concentration—
pH7.2Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-07-24Storage / measurement temperature— / 20.0
Exposure time3.0Frames600
Wavelength0.103Sample-to-detector distance1.5
SourceX-ray synchrotronDetectorPilatus3 X 2M
Facility / beamlineAdvanced Light Source (ALS) / 12.3.1 (SIBYLS) · Berkeley, CA, USA
q range0.131 – 5.608Sample 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
codeSASDE89
statusPublished
type_of_curveSEC-SAS
angular_unit1/A
project.titleFunctional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling.
project.publication.titleFunctional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling.
project.publication.author_listGe J, Remesh SG, Hammel M, Pan S, Mahan AD, Wang S, Wang X
project.publication.journalStructure
project.publication.doi10.1016/j.str.2019.05.011
project.publication.pmid31257107
project.publication.published_date2019 Aug 6
project.statusreleased
project.submitted_date2018-12-11
project.released_date2019-09-13
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experiment.instrument.detector.resolution172.0
experiment.instrument.nameAdvanced Light Source (ALS)
experiment.instrument.cityBerkeley, CA
experiment.instrument.countryUSA
experiment.instrument.beamline_name12.3.1 (SIBYLS)
experiment.instrument.beam_geometry
experiment.instrument.type_of_sourceX-ray synchrotron
experiment.instrument.point_sourcenull
experiment.instrument.line_collimationnull
experiment.instrument.sample_path_lengthnull
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experiment.sample.molecule[0].long_nameInterleukin-1 receptor accessory protein ectodomains with RII linker
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceSERCDDWGLDTMRQIQVFEDEPARIKCPLFEHFLKFNYSTAHSAGLTLIWYWTRQDRDLEEPINFRLPENRISKEKDVLWFRPTLLNDTGNYTCMLRNTTYCSKVAFPLEVVQKDSCFNSPMKLPVHKLYIEYGIQRITCPNVDGYFPSSVKPTITWYMGCYKIQNFNNVIPEGMNLSFLIALISNNGNYTCVVTYPENGRTFHLTRTLTVKVKKKKEETIPVIHSPNDHVVYEKEPGEELLIPCTVYFSFLMDSRNEVWWTIDGKKPDDITIDVTINESISHSRTEDETRTQILSIKKVTSEDLKRSYVCHARSAKGEVAKAAKVKAAALHHILDAQKMVWNHRHHHHHH
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ9NPH3
experiment.sample.molecule[0].uniprot_range_first21
experiment.sample.molecule[0].uniprot_range_last348
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMTLLWCVVSLYFYGILQSDASERCDDWGLDTMRQIQVFEDEPARIKCPLFEHFLKFNYST AHSAGLTLIWYWTRQDRDLEEPINFRLPENRISKEKDVLWFRPTLLNDTGNYTCMLRNTT YCSKVAFPLEVVQKDSCFNSPMKLPVHKLYIEYGIQRITCPNVDGYFPSSVKPTITWYMG CYKIQNFNNVIPEGMNLSFLIALISNNGNYTCVVTYPENGRTFHLTRTLTVKVVGSPKNA VPPVIHSPNDHVVYEKEPGEELLIPCTVYFSFLMDSRNEVWWTIDGKKPDDITIDVTINE SISHSRTEDETRTQILSIKKVTSEDLKRSYVCHARSAKGEVAKAAKVKQKVPAPRYTVEL ACGFGATVLLVVILIVVYHVYWLEMVLFYRAHFGTDETILDGKEYDIYVSYARNAEEEEF VLLTLRGVLENEFGYKLCIFDRDSLPGGIVTDETLSFIQKSRRLLVVLSPNYVLQGTQAL LELKAGLENMASRGNINVILVQYKAVKETKVKELKRAKTVLTVIKWKGEKSKYPQGRFWK QLQVAMPVKKSPRRSSSDEQGLSYSSLKNV
experiment.sample.molecule[0].mw40.893
experiment.sample.molecule[0].total_mw40.893
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
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experiment.sample.ext_coefficientnull
experiment.sample.contrastnull
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experiment.contributor[0].affiliation[0].short_namenull
experiment.contributor[0].affiliation[0].addressTaiwan
experiment.contributor[0].affiliation[0].full_nameNational Cheng Kung University
experiment.contributor[0].affiliation[0].webpagehttp://www.ncku.edu.tw/
experiment.contributor[0].contributor_nameShu-Ying
experiment.contributor[0].contributor_surnameWang
experiment.contributor[0].orcid
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-07-24
experiment.storage_temperaturenull
experiment.cell_temperature20.0
experiment.exposure_time3.0
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experiment.wavelength0.103
experiment.sample_detector_distance1.5
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experiment.concentration_max7.8
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experiment.flow_ratenull
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pddf_softwareATSAS GNOM
pddf_software_version4.5a
i0_calibration_standardnull
descriptionSEC-SAXS was performed at 20°C using the following parameters: Column: Schodex kw-803 ; Flow rate: 0.5 mL/min; Total acquisition time: 30min; Sample injection concentration: 7.8 mg/mL; Injection volume: 50 μL.
experiment_descriptionSynchrotron SAXS data from solutions of Interleukin-1 receptor accessory protein ectodomain with RII linker in 10mM HEPES, 150mM NaCl, 3% glycerol, pH 7.2 were measured using size-exclusion chromatography SAXS (SEC-SAXS) on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.103 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data were collected as 600 successive 3 second frames through the SEC elution profile. Sample-elution peak data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.
tags[]
intensity_unitarbitrary
experimental_mw50.2
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
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pddf_i0_errornull
guinier_i0342.7
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pddf_rg3.12
pddf_rg_errornull
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guinier_rg_error0.1
pddf_dmax10.66
pddf_dmax_errornull
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porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
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guinier_point_last54
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDE89_datloglog_img.png
symmetrynull
last_modified2020-11-27T12:00:32.590807+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDE89
statussuccess
started_at2026-08-11T16:46:01.401863+00:00
finished_at2026-08-11T16:46:10.476304+00:00
source_last_modified2020-11-27T12:00:32.590807+01:00
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View the complete summary.json source
{
  "code": "SASDE89",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling.",
    "publication": {
      "title": "Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling.",
      "author_list": "Ge J, Remesh SG, Hammel M, Pan S, Mahan AD, Wang S, Wang X",
      "journal": "Structure",
      "doi": "10.1016/j.str.2019.05.011",
      "pmid": "31257107",
      "published_date": "2019 Aug 6"
    },
    "status": "released",
    "submitted_date": "2018-12-11",
    "released_date": "2019-09-13"
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          "long_name": "Interleukin-1 receptor accessory protein ectodomains with RII linker",
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        "comment": null,
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    },
    "contributor": [
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        "affiliation": [
          {
            "short_name": null,
            "address": "Taiwan",
            "full_name": "National Cheng Kung University",
            "webpage": "http://www.ncku.edu.tw/"
          }
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        "contributor_name": "Shu-Ying",
        "contributor_surname": "Wang",
        "orcid": ""
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    "concentration_unit": null,
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    "total_exposure_time": null,
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View the complete manifest.json source
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