SASDVT4

Endophilin B1 wild type (0.14 mg/ml)

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2025-02-05T17:23:18.368460+01:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Endophilin B1 wild type (0.14 mg/ml)

Concentration— – 0.69 Buffer / pH20 mM HEPES, 150 mM NaCl, 1 mM TCEP, 0.5 mM DTT / 8.1
Experimental temperature4.0 Facility / beamlineESRF / BM29
Wavelength0.09918 nmExposure1.0 s × 15

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Endophilin-B1
View sequence
MNIMDFNVKKLAADAGTFLSRAVQFTEEKLGQAEKTELDAHLENLLSKAECTKIWTEKIMKQTEVLLQPNPNARIEEFVYEKLDRKAPSRINNPELLGQYMIDAGTEFGPGTAYGNALIKCGETQKRIGTADRELIQTSALNFLTPLRNFIEGDYKTIAKERKLLQNKRLDLDAAKTRLKKAKAAETRNSSEQELRITQSEFDRQAEITRLLLEGISSTHAHHLRCLNDFVEAQMTYYAQCYQYMLDLQKQLGSFPSNYLSNNNQTSVTPVPSVLPNAIGSSAMASTSGLVITSPSNLSDLKECSGSRKARVLYDYDAANSTELSLLADEVITVFSVVGMDSDWLMGERGNQKGKVPITYLELLN
proteinHomo sapiensQ9Y3711–365monomerMolecule count 140.796 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11000[3]0.008509853–0.4953721 1/AHas uncertainty columnMissing 0238sasbdb/entries/t4/sasdvt4/source/SASDVT4.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)15.3—Å
i0Guinier43.0065—1/cm
i0P(r)45.16—1/cm
mwExperimental36.9—kDa
mwPorod29.0—kDa
porod_volumePorod47.0—ų
rgGuinier3.6880.956Å
rgP(r)4.27—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

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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 HEPES, 150 mM NaCl, 1 mM TCEP, 0.5 mM DTTBuffer concentration—
pH8.1Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2024-03-10Storage / measurement temperature4.0 / 4.0
Exposure time1.0Frames15
Wavelength0.09918Sample-to-detector distance2.827
SourceX-ray synchrotronDetectorPilatus3 2M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.085 – 4.954Sample 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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pddf:source record
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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
codeSASDVT4
statusPublished
type_of_curveSingle concentration
angular_unit1/A
project.titlePeripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers
project.publication.titlePeripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers
project.publication.author_listThorlacius A, Rulev M, Sundberg O, Sundborger-Lunna A
project.publication.journalCommunications Biology
project.publication.doi10.1038/s42003-025-07610-1
project.publication.pmidnull
project.publication.published_date2025 Feb 05
project.statusreleased
project.submitted_date2024-07-12
project.released_date2025-01-28
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experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus3 2M
experiment.instrument.detector.resolution0.172
experiment.instrument.nameESRF
experiment.instrument.cityGrenoble
experiment.instrument.countryFrance
experiment.instrument.beamline_nameBM29
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_nameEndophilin-B1
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMNIMDFNVKKLAADAGTFLSRAVQFTEEKLGQAEKTELDAHLENLLSKAECTKIWTEKIM KQTEVLLQPNPNARIEEFVYEKLDRKAPSRINNPELLGQYMIDAGTEFGPGTAYGNALIK CGETQKRIGTADRELIQTSALNFLTPLRNFIEGDYKTIAKERKLLQNKRLDLDAAKTRLK KAKAAETRNSSEQELRITQSEFDRQAEITRLLLEGISSTHAHHLRCLNDFVEAQMTYYAQ CYQYMLDLQKQLGSFPSNYLSNNNQTSVTPVPSVLPNAIGSSAMASTSGLVITSPSNLSD LKECSGSRKARVLYDYDAANSTELSLLADEVITVFSVVGMDSDWLMGERGNQKGKVPITY LELLN
experiment.sample.molecule[0].organismHomo sapiens
experiment.sample.molecule[0].uniprot_codeQ9Y371
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last365
experiment.sample.molecule[0].oligomerizationmonomer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMNIMDFNVKKLAADAGTFLSRAVQFTEEKLGQAEKTELDAHLENLLSKAECTKIWTEKIM KQTEVLLQPNPNARIEEFVYEKLDRKAPSRINNPELLGQYMIDAGTEFGPGTAYGNALIK CGETQKRIGTADRELIQTSALNFLTPLRNFIEGDYKTIAKERKLLQNKRLDLDAAKTRLK KAKAAETRNSSEQELRITQSEFDRQAEITRLLLEGISSTHAHHLRCLNDFVEAQMTYYAQ CYQYMLDLQKQLGSFPSNYLSNNNQTSVTPVPSVLPNAIGSSAMASTSGLVITSPSNLSD LKECSGSRKARVLYDYDAANSTELSLLADEVITVFSVVGMDSDWLMGERGNQKGKVPITY LELLN
experiment.sample.molecule[0].mw40.796
experiment.sample.molecule[0].total_mw40.796
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_description
experiment.sample.buffer.name20 mM HEPES, 150 mM NaCl, 1 mM TCEP, 0.5 mM DTT
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph8.1
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameEndophilin B1 wild type (0.14 mg/ml)
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_nameUppsala University
experiment.contributor[0].affiliation[0].webpagenull
experiment.contributor[0].contributor_nameMaksim
experiment.contributor[0].contributor_surnameRulev
experiment.contributor[0].orcidhttps://orcid.org/0000-0001-6103-320X
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2024-03-10
experiment.storage_temperature4.0
experiment.cell_temperature4.0
experiment.exposure_time1.0
experiment.number_of_frames15
experiment.wavelength0.09918
experiment.sample_detector_distance2.827
experiment.concentration_minnull
experiment.concentration_max0.69
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.085
experiment.s_max4.954
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of endophilin B1 in 20 mM HEPES, 150 mM NaCl, 1 mM TCEP, 0.5 mM DTT, pH 8.1 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus3 2M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.09918 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 0.69 mg/ml was measured at 4°C. 15 successive 1 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[]
intensity_unit1/cm
experimental_mw36.9
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw29.0
porod_mw_errornull
pddf_i045.16
pddf_i0_errornull
guinier_i043.0065
guinier_i0_errornull
pddf_rg4.27
pddf_rg_errornull
guinier_rg3.688
guinier_rg_error0.956
pddf_dmax15.3
pddf_dmax_errornull
porod_volume47.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first8
guinier_point_last57
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDVT4_datloglog_img.png
symmetrynull
last_modified2025-02-05T17:23:18.368460+01:00
bragg_peak[]
manifest.json:34 field values
Field pathRaw value
codeSASDVT4
statussuccess
started_at2026-08-11T14:31:13.667904+00:00
finished_at2026-08-11T14:31:22.292965+00:00
source_last_modified2025-02-05T17:23:18.368460+01:00
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View the complete summary.json source
{
  "code": "SASDVT4",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/A",
  "project": {
    "title": "Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers",
    "publication": {
      "title": "Peripheral membrane protein endophilin B1 probes, perturbs and permeabilizes lipid bilayers",
      "author_list": "Thorlacius A, Rulev M, Sundberg O, Sundborger-Lunna A",
      "journal": "Communications Biology",
      "doi": "10.1038/s42003-025-07610-1",
      "pmid": null,
      "published_date": "2025 Feb 05"
    },
    "status": "released",
    "submitted_date": "2024-07-12",
    "released_date": "2025-01-28"
  },
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    "sample": {
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          "long_name": "Endophilin-B1",
          "short_name": null,
          "sequence": "MNIMDFNVKKLAADAGTFLSRAVQFTEEKLGQAEKTELDAHLENLLSKAECTKIWTEKIM\r\nKQTEVLLQPNPNARIEEFVYEKLDRKAPSRINNPELLGQYMIDAGTEFGPGTAYGNALIK\r\nCGETQKRIGTADRELIQTSALNFLTPLRNFIEGDYKTIAKERKLLQNKRLDLDAAKTRLK\r\nKAKAAETRNSSEQELRITQSEFDRQAEITRLLLEGISSTHAHHLRCLNDFVEAQMTYYAQ\r\nCYQYMLDLQKQLGSFPSNYLSNNNQTSVTPVPSVLPNAIGSSAMASTSGLVITSPSNLSD\r\nLKECSGSRKARVLYDYDAANSTELSLLADEVITVFSVVGMDSDWLMGERGNQKGKVPITY\r\nLELLN",
          "organism": "Homo sapiens",
          "uniprot_code": "Q9Y371",
          "uniprot_range_first": 1,
          "uniprot_range_last": 365,
          "oligomerization": "monomer",
          "molecular_type": "protein",
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          "mw": 40.796,
          "total_mw": 40.796,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": ""
        }
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        "concentration_unit": null,
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        "deuteration": null
      },
      "purity_method": null,
      "name": "Endophilin B1 wild type (0.14 mg/ml)",
      "ext_coefficient": null,
      "contrast": null,
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      "absorbption": null,
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      "mixture": null
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            "short_name": null,
            "address": null,
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    "concentration_method": null,
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View the complete manifest.json source
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