SASDC82

Rab family protein CtRoco nucleotide free

Data type: SASBDB experimental data Status: Published Curve type: Other Last updated: 2019-12-06T13:07:15.624532+01:00
▼

1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Rab family protein CtRoco nucleotide free

Concentration1.0 – 2.0 Buffer / pH20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT / 7.5
Experimental temperature25.0 Facility / beamlineESRF / BM29
Wavelength0.099 nmExposure— s × 55

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Rab family protein
View sequence
MSYYHHHHHHDYDIPTTENLYFQGAMGSMSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLESLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSLSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAPLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPPEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPKESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISCKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDELVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGNPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAENAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYYNNVAPFFDLPSVPPVLLGKEKT
proteinChlorobaculum tepidumQ8KC981–1102dimerMolecule count 2127.147 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11043[3]0.0320823–4.97517 1/nmHas uncertainty columnMissing 04sasbdb/entries/82/sasdc82/source/SASDC82.dat
▼

2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)18.39—nm
i0Guinier125.130.0625—
i0P(r)125.40.06—
mwExperimental246.0—kDa
mwPorod259.0—kDa
porod_volumePorod440.41—nm³
rgGuinier4.980.004nm
rgP(r)5.040.004nm

These values are reported by SASBDB; SAXSdb did not recalculate them from the experimental curve.

▼

3. Source Fits and Models Source Fits & Models

▶

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 name20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTTBuffer concentration—
pH7.5Additives—
Buffer description—
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2015-02-16Storage / measurement temperature— / 25.0
Exposure time—Frames55
Wavelength0.099Sample-to-detector distance—
SourceX-ray synchrotronDetectorPilatus 1M
Facility / beamlineESRF / BM29 · Grenoble, France
q range0.032 – 4.975Sample 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

CategoryFileStatusSizeChecksumDownload and View
curvesasbdb/entries/82/sasdc82/source/SASDC82.datdownloaded57480cf1e45f7bfde04f04e71ec01f415679454b4e0d6af15210b9076c4b5bedf6f11DownloadView source fileSource site
full_entry_zipsasbdb/entries/82/sasdc82/source/SASDC82.zipdownloaded31935a124e8cde13b7165623634851f57ee5af14bbf57bd602819e83040fee12da61fDownloadView source fileSource site
pddfsasbdb/entries/82/sasdc82/source/SASDC82.outdownloaded315449669776a75d51d44d654dabed59050a57a5e63471eb9e313a8bf3baecda9ad9bDownloadView source fileSource site
sascifsasbdb/entries/82/sasdc82/source/SASDC82.sascifdownloaded163108b3bc484295454ba6744de64492e92dc981bd6289b777abc0253aa13128cd8c62DownloadView source fileSource site
summarysasbdb/entries/82/sasdc82/source/summary.jsondownloaded96223e07fc4a6410a8b2c69a3baaeed83ff4153f6166b49017fe57331fa0dc14caa5DownloadView source fileSource site
curve:source record
{
  "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.dat",
  "role": "curve",
  "sha256": "cf1e45f7bfde04f04e71ec01f415679454b4e0d6af15210b9076c4b5bedf6f11",
  "size": 57480,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/intensities_files/SASDC82.dat"
}
full_entry_zip:source record and ZIP contents (4 items)
{
  "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.zip",
  "role": "full_entry_zip",
  "sha256": "a124e8cde13b7165623634851f57ee5af14bbf57bd602819e83040fee12da61f",
  "size": 31935,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/zip_directories/SASDC82.zip",
  "zip_member_count": 4,
  "zip_members": [
    {
      "crc32": "223974a5",
      "name": "SASDC82/experimental_data/SASDC82.dat",
      "size": 57480
    },
    {
      "crc32": "7fcc69eb",
      "name": "SASDC82/pddf/SASDC82.out",
      "size": 31544
    },
    {
      "crc32": "d8f86c72",
      "name": "SASDC82/SASDC82_fit1.fir",
      "size": 18977
    },
    {
      "crc32": "4f9fe3c2",
      "name": "SASDC82/SASDC82_fit1_model1.pdb",
      "size": 47139
    }
  ],
  "zip_validation": "central_directory_readable"
}
pddf:source record
{
  "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.out",
  "role": "pddf",
  "sha256": "9669776a75d51d44d654dabed59050a57a5e63471eb9e313a8bf3baecda9ad9b",
  "size": 31544,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/p_of_R_files/SASDC82.out"
}
sascif:source record
{
  "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.sascif",
  "role": "sascif",
  "sha256": "b3bc484295454ba6744de64492e92dc981bd6289b777abc0253aa13128cd8c62",
  "size": 163108,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC82.sascif"
}
summary:source record
{
  "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/summary.json",
  "sha256": "3e07fc4a6410a8b2c69a3baaeed83ff4153f6166b49017fe57331fa0dc14caa5",
  "size": 9622,
  "status": "downloaded",
  "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDC82/"
}

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
codeSASDC82
statusPublished
type_of_curveOther
angular_unit1/nm
project.titleA homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.
project.publication.titleA homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.
project.publication.author_listDeyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W
project.publication.journalNat Commun
project.publication.doi10.1038/s41467-017-01103-4
project.publication.pmid29044096
project.publication.published_date2017 Oct 18
project.statusreleased
project.submitted_date2017-03-21
project.released_date2017-10-20
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDC82.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDC82.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC82_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDC82.sascif
experiment.instrument.detector.typeDectris
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
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_nameRab family protein
experiment.sample.molecule[0].short_nameCtRoco
experiment.sample.molecule[0].sequenceMSYYHHHHHHDYDIPTTENLYFQGAMGSMSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLESLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSLSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAPLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPPEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPKESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISCKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDELVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGNPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAENAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYYNNVAPFFDLPSVPPVLLGKEKT
experiment.sample.molecule[0].organismChlorobaculum tepidum
experiment.sample.molecule[0].uniprot_codeQ8KC98
experiment.sample.molecule[0].uniprot_range_first1
experiment.sample.molecule[0].uniprot_range_last1102
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLE SLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKIS DIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSL SSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKS LTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAP LASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQ ISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPP EIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPK ESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLL DSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISC KNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICND SGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLN TSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNL PTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEG ALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDE LVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGN PTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAE NAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYY NNVAPFFDLPSVPPVLLGKEKT
experiment.sample.molecule[0].mw127.147
experiment.sample.molecule[0].total_mw254.294
experiment.sample.molecule[0].number_molecules2
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 HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 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.ph7.5
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.nameRab family protein CtRoco nucleotide free
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_nameVUB
experiment.contributor[0].affiliation[0].addressPleinlaan 2 1050 Brussel
experiment.contributor[0].affiliation[0].full_nameVrije Universiteit Brussel
experiment.contributor[0].affiliation[0].webpagehttp://www.vub.ac.be/
experiment.contributor[0].contributor_nameEgon
experiment.contributor[0].contributor_surnameDeyaert
experiment.contributor[0].orcidnull
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2015-02-16
experiment.storage_temperaturenull
experiment.cell_temperature25.0
experiment.exposure_timenull
experiment.number_of_frames55
experiment.wavelength0.099
experiment.sample_detector_distancenull
experiment.concentration_min1.0
experiment.concentration_max2.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.032
experiment.s_max4.975
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDC82_fit1_model1_img.png
fits[0].models[0].softwareDAMMIN
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modeldummy
fits[0].models[0].software_version5.3
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDC82_fit1_model1.pdb
fits[0].models[0].model_mw283.95
fits[0].models[0].bead_radius5.5
fits[0].models[0].loghttps://www.sasbdb.org/media/log_files/refine_kEg200J.log
fits[0].models[0].symmetryP2
fits[0].models[0].comment
fits[0].models[0].user98
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC82_fit1_fit_img.png
fits[0].softwareDAMMIN
fits[0].chi_square_value9.3
fits[0].p_value0.078515
fits[0].fit_residual_plotSASDC82_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDC82_fit1.fir
fits[0].fit_loghttps://www.sasbdb.org/media/fitting_files/log_files/refine_eK7rGlo.log
fits[0].software_version5.3
fits[0].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionGNOM 4.6
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of Rab family protein CtRoco (nucleotide free) in 20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT, pH 7.5 were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a Pilatus 1M detector at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Inline SEC-SAXS was employed at 25°C (50 µl injection volume of an 8 mg/ml protein solution on a Bio SEC-3 HPLC column (Agilent, 3 µm 300 Å)). 55 successive frames were collected through the elution peak. 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 and averaged to produce the final SAXS data displayed in this entry.
tags[]
intensity_unitnull
experimental_mw246.0
experimental_mw_errornull
guinier_i0_mwnull
guinier_i0_mw_errornull
porod_mw259.0
porod_mw_errornull
pddf_i0125.4
pddf_i0_error0.06
guinier_i0125.13
guinier_i0_error0.0625
pddf_rg5.04
pddf_rg_error0.004
guinier_rg4.98
guinier_rg_error0.004
pddf_dmax18.39
pddf_dmax_errornull
porod_volume440.41
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first7
guinier_point_last49
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDC82_datloglog_img.png
symmetrynull
last_modified2019-12-06T13:07:15.624532+01:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDC82
statussuccess
started_at2026-08-11T13:32:29.371590+00:00
finished_at2026-08-11T13:32:39.637281+00:00
source_last_modified2019-12-06T13:07:15.624532+01:00
files[0].statusdownloaded
files[0].urlhttps://www.sasbdb.org/rest-api/entry/summary/SASDC82/
files[0].path/data/saxsdb/sasbdb/entries/82/sasdc82/source/summary.json
files[0].size9622
files[0].sha2563e07fc4a6410a8b2c69a3baaeed83ff4153f6166b49017fe57331fa0dc14caa5
files[1].statusdownloaded
files[1].urlhttps://www.sasbdb.org/media/intensities_files/SASDC82.dat
files[1].path/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.dat
files[1].size57480
files[1].sha256cf1e45f7bfde04f04e71ec01f415679454b4e0d6af15210b9076c4b5bedf6f11
files[1].rolecurve
files[2].statusdownloaded
files[2].urlhttps://www.sasbdb.org/media/p_of_R_files/SASDC82.out
files[2].path/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.out
files[2].size31544
files[2].sha2569669776a75d51d44d654dabed59050a57a5e63471eb9e313a8bf3baecda9ad9b
files[2].rolepddf
files[3].statusdownloaded
files[3].urlhttps://www.sasbdb.org/media/sascif/sascif_files/SASDC82.sascif
files[3].path/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.sascif
files[3].size163108
files[3].sha256b3bc484295454ba6744de64492e92dc981bd6289b777abc0253aa13128cd8c62
files[3].rolesascif
files[4].statusdownloaded
files[4].urlhttps://www.sasbdb.org/media/zip_directories/SASDC82.zip
files[4].path/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.zip
files[4].size31935
files[4].sha256a124e8cde13b7165623634851f57ee5af14bbf57bd602819e83040fee12da61f
files[4].rolefull_entry_zip
files[4].zip_member_count4
files[4].zip_validationcentral_directory_readable
View the complete summary.json source
{
  "code": "SASDC82",
  "status": "Published",
  "type_of_curve": "Other",
  "angular_unit": "1/nm",
  "project": {
    "title": "A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.",
    "publication": {
      "title": "A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.",
      "author_list": "Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W",
      "journal": "Nat Commun",
      "doi": "10.1038/s41467-017-01103-4",
      "pmid": "29044096",
      "published_date": "2017 Oct 18"
    },
    "status": "released",
    "submitted_date": "2017-03-21",
    "released_date": "2017-10-20"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC82.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC82.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC82_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC82_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC82.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "ESRF",
      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "beam_geometry": "",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
      "line_collimation_slitlength": null,
      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Rab family protein",
          "short_name": "CtRoco",
          "sequence": "MSYYHHHHHHDYDIPTTENLYFQGAMGSMSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLESLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSLSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAPLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPPEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPKESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISCKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDELVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGNPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAENAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYYNNVAPFFDLPSVPPVLLGKEKT",
          "organism": "Chlorobaculum tepidum",
          "uniprot_code": "Q8KC98",
          "uniprot_range_first": 1,
          "uniprot_range_last": 1102,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLE\nSLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKIS\nDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSL\nSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKS\nLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAP\nLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQ\nISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPP\nEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPK\nESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLL\nDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISC\nKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICND\nSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLN\nTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNL\nPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEG\nALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDE\nLVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGN\nPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAE\nNAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYY\nNNVAPFFDLPSVPPVLLGKEKT",
          "mw": 127.147,
          "total_mw": 254.294,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Rab family protein CtRoco nucleotide free",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "VUB",
            "address": "Pleinlaan 2 1050 Brussel ",
            "full_name": "Vrije Universiteit Brussel",
            "webpage": "http://www.vub.ac.be/"
          }
        ],
        "contributor_name": "Egon",
        "contributor_surname": "Deyaert",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-02-16",
    "storage_temperature": null,
    "cell_temperature": 25.0,
    "exposure_time": null,
    "number_of_frames": 55,
    "wavelength": 0.099,
    "sample_detector_distance": null,
    "concentration_min": 1.0,
    "concentration_max": 2.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.032,
    "s_max": 4.975,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC82_fit1_model1_img.png",
          "software": "DAMMIN",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": "5.3",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC82_fit1_model1.pdb",
          "model_mw": 283.95,
          "bead_radius": 5.5,
          "log": "https://www.sasbdb.org/media/log_files/refine_kEg200J.log",
          "symmetry": "P2",
          "comment": "",
          "user": 98
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC82_fit1_fit_img.png",
      "software": "DAMMIN",
      "chi_square_value": 9.3,
      "p_value": 0.078515,
      "fit_residual_plot": "SASDC82_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC82_fit1.fir",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_eK7rGlo.log",
      "software_version": "5.3",
      "description": null
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "GNOM 4.6",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Rab family protein CtRoco (nucleotide free) in 20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT, pH 7.5 were collected on the BM29 camera on the storage ring ESRF (Grenoble, France) using a Pilatus 1M detector at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Inline SEC-SAXS was employed at 25°C (50 µl injection volume of an 8 mg/ml protein solution on a Bio SEC-3 HPLC column (Agilent, 3 µm 300 Å)). 55 successive frames were collected through the elution peak. 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 and averaged to produce the final SAXS data displayed in this entry.",
  "tags": [],
  "intensity_unit": null,
  "experimental_mw": 246.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 259.0,
  "porod_mw_error": null,
  "pddf_i0": 125.4,
  "pddf_i0_error": 0.06,
  "guinier_i0": 125.13,
  "guinier_i0_error": 0.0625,
  "pddf_rg": 5.04,
  "pddf_rg_error": 0.004,
  "guinier_rg": 4.98,
  "guinier_rg_error": 0.004,
  "pddf_dmax": 18.39,
  "pddf_dmax_error": null,
  "porod_volume": 440.41,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 7,
  "guinier_point_last": 49,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDC82_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}
View the complete manifest.json source
{
  "code": "SASDC82",
  "status": "success",
  "started_at": "2026-08-11T13:32:29.371590+00:00",
  "finished_at": "2026-08-11T13:32:39.637281+00:00",
  "source_last_modified": "2019-12-06T13:07:15.624532+01:00",
  "files": [
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDC82/",
      "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/summary.json",
      "size": 9622,
      "sha256": "3e07fc4a6410a8b2c69a3baaeed83ff4153f6166b49017fe57331fa0dc14caa5"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/intensities_files/SASDC82.dat",
      "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.dat",
      "size": 57480,
      "sha256": "cf1e45f7bfde04f04e71ec01f415679454b4e0d6af15210b9076c4b5bedf6f11",
      "role": "curve"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/p_of_R_files/SASDC82.out",
      "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.out",
      "size": 31544,
      "sha256": "9669776a75d51d44d654dabed59050a57a5e63471eb9e313a8bf3baecda9ad9b",
      "role": "pddf"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC82.sascif",
      "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.sascif",
      "size": 163108,
      "sha256": "b3bc484295454ba6744de64492e92dc981bd6289b777abc0253aa13128cd8c62",
      "role": "sascif"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/zip_directories/SASDC82.zip",
      "path": "/data/saxsdb/sasbdb/entries/82/sasdc82/source/SASDC82.zip",
      "size": 31935,
      "sha256": "a124e8cde13b7165623634851f57ee5af14bbf57bd602819e83040fee12da61f",
      "role": "full_entry_zip",
      "zip_member_count": 4,
      "zip_validation": "central_directory_readable"
    }
  ]
}