SASDEF5

Phosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-06-21T07:56:39.492710+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Phosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0

Concentration— – 8.0 Buffer / pH20mM potassium phosphate 150mM NaCl 0.007 %(w/v) β-octyl glucoside 1mM DTT 1mM MgCl 1mM thiaminpyrophosphate 2 %(v/v) glycerol / 7.0
Experimental temperature20.0 Facility / beamlinePETRA III / EMBL P12
Wavelength0.124 nmExposure0.045 s × 29

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Probable phosphoketolase
View sequence
MSHHHHHHSMDIEFVDLEGSMTEYNSEAYLKKLDKWWRAATYLGAGMIFLKENPLFSVTGTPIKAENLKANPIGHWGTVSGQTFLYAHANRLINKYDQKMFYMGGPGHGGQAMVVPSYLDGSYTEAYPEITQDLEGMSRLFKRFSFPGGIGSHMTAQTPGSLHEGGELGYVLSHATGAILDQPEQIAFAVVGDGEAETGPLMTSWHSIKFINPKNDGAILPILDLNGFKISNPTLFARTSDVDIRKFFEGLGYSPRYIENDDIHDYMAYHKLAAEVFDKAIEDIHQIQKDAREDNRYQNGEIPAWPIVIARLPKGWGGPRYNDWSGPKFDGKGMPIEHSFRAHQVPLPLSSKNMGTLPEFVKWMTSYQPETLFNADGSLKEELRDFAPKGEMRMASNPVTNGGVDSSNLVLPDWQEFANPISENNRGKLLPDTNDNMDMNVLSKYFAEIVKLNPTRFRLFGPDETMSNRFWEMFKVTNRQWMQVIKNPNDEFISPEGRIIDSQLSEHQAEGWLEGYTLTGRTGAFASYESFLRVVDSMLTQHFKWIRQAADQKWRHDYPSLNVISTSTVFQQDHNGYTHQDPGMLTHLAEKKSDFIRQYLPADGNTLLAVFDRAFQDRSKINHIVASKQPRQQWFTKEEAEKLATDGIATIDWASTAKDGEAVDLVFASAGAEPTIETLAALHLVNEVFPQAKFRYVNVVELGRLQKKKGALNQERELSDEEFEKYFGPSGTPVIFGFHGYEDLIESIFYQRGHDGLIVHGYREDGDITTTYDMRVYSELDRFHQAIDAMQVLYVNRKVNQGLAKAFIDRMKRTLVKHFEVTRNEGVDIPDFTEWVWSDLKK
proteinLactococcus lactis subsp. lactisQ9CFH4—–—dimerMolecule count 295.727 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
11827[3]0.0249287–5.06402 1/nmHas uncertainty columnMissing 017sasbdb/entries/f5/sasdef5/source/SASDEF5.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)10.15—nm
i0Guinier21282.014.31/cm
i0P(r)21180.0—1/cm
mwExperimental164.0—kDa
mwGuinier I(0)146.0—kDa
mwPorod148.0—kDa
porod_volumePorod237.0—nm³
rgGuinier3.440.55nm
rgP(r)3.387—nm

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 name20mM potassium phosphate 150mM NaCl 0.007 %(w/v) β-octyl glucoside 1mM DTT 1mM MgCl 1mM thiaminpyrophosphate 2 %(v/v) glycerolBuffer concentration—
pH7.0Additives—
Buffer descriptionSEC11 buffer
Purity measurement method—Extinction coefficient—
Absorbance—Scattering contrast—
Specific volume / dry volume— / —Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2017-09-07Storage / measurement temperature20.0 / 20.0
Exposure time0.045Frames29
Wavelength0.124Sample-to-detector distance3.0
SourceX-ray synchrotronDetectorPilatus 2M
Facility / beamlinePETRA III / EMBL P12 · DESY; Hamburg, Germany
q range0.025 – 5.064Sample 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:182 field values
Field pathRaw value
codeSASDEF5
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleCrystal structure of a xylulose 5-phosphate phosphoketolase. insights into the substrate specificity for xylulose 5-phosphate.
project.publication.titleCrystal structure of a xylulose 5-phosphate phosphoketolase. insights into the substrate specificity for xylulose 5-phosphate.
project.publication.author_listScheidig AJ, Horvath D, Szedlacsek SE
project.publication.journalJ Struct Biol
project.publication.doi10.1016/j.jsb.2019.04.017
project.publication.pmid31059775
project.publication.published_date2019 May 3
project.statusreleased
project.submitted_date2018-09-30
project.released_date2019-05-08
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDEF5.out
intensities_datahttps://www.sasbdb.org/media/intensities_files/SASDEF5.dat
intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF5_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF5_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEF5_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEF5_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDEF5.sascif
experiment.instrument.detector.typenull
experiment.instrument.detector.namePilatus 2M
experiment.instrument.detector.resolutionnull
experiment.instrument.namePETRA III
experiment.instrument.cityDESY; Hamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL P12
experiment.instrument.beam_geometrynull
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_nameProbable phosphoketolase
experiment.sample.molecule[0].short_namenull
experiment.sample.molecule[0].sequenceMSHHHHHHSMDIEFVDLEGSMTEYNSEAYLKKLDKWWRAATYLGAGMIFLKENPLFSVTGTPIKAENL KANPIGHWGTVSGQTFLYAHANRLINKYDQKMFYMGGPGHGGQAMVVPSYLDGSYTEAY PEITQDLEGMSRLFKRFSFPGGIGSHMTAQTPGSLHEGGELGYVLSHATGAILDQPEQI AFAVVGDGEAETGPLMTSWHSIKFINPKNDGAILPILDLNGFKISNPTLFARTSDVDIR KFFEGLGYSPRYIENDDIHDYMAYHKLAAEVFDKAIEDIHQIQKDAREDNRYQNGEIPA WPIVIARLPKGWGGPRYNDWSGPKFDGKGMPIEHSFRAHQVPLPLSSKNMGTLPEFVKW MTSYQPETLFNADGSLKEELRDFAPKGEMRMASNPVTNGGVDSSNLVLPDWQEFANPIS ENNRGKLLPDTNDNMDMNVLSKYFAEIVKLNPTRFRLFGPDETMSNRFWEMFKVTNRQW MQVIKNPNDEFISPEGRIIDSQLSEHQAEGWLEGYTLTGRTGAFASYESFLRVVDSMLT QHFKWIRQAADQKWRHDYPSLNVISTSTVFQQDHNGYTHQDPGMLTHLAEKKSDFIRQY LPADGNTLLAVFDRAFQDRSKINHIVASKQPRQQWFTKEEAEKLATDGIATIDWASTAK DGEAVDLVFASAGAEPTIETLAALHLVNEVFPQAKFRYVNVVELGRLQKKKGALNQERE LSDEEFEKYFGPSGTPVIFGFHGYEDLIESIFYQRGHDGLIVHGYREDGDITTTYDMRV YSELDRFHQAIDAMQVLYVNRKVNQGLAKAFIDRMKRTLVKHFEVTRNEGVDIPDFTEW VWSDLKK
experiment.sample.molecule[0].organismLactococcus lactis subsp. lactis
experiment.sample.molecule[0].uniprot_codeQ9CFH4
experiment.sample.molecule[0].uniprot_range_firstnull
experiment.sample.molecule[0].uniprot_range_lastnull
experiment.sample.molecule[0].oligomerizationdimer
experiment.sample.molecule[0].molecular_typeprotein
experiment.sample.molecule[0].uniprot_sequenceMTEYNSEAYLKKLDKWWRAATYLGAGMIFLKENPLFSVTGTPIKAENLKANPIGHWGTVS GQTFLYAHANRLINKYDQKMFYMGGPGHGGQAMVVPSYLDGSYTEAYPEITQDLEGMSRL FKRFSFPGGIGSHMTAQTPGSLHEGGELGYVLSHATGAILDQPEQIAFAVVGDGEAETGP LMTSWHSIKFINPKNDGAILPILDLNGFKISNPTLFARTSDVDIRKFFEGLGYSPRYIEN DDIHDYMAYHKLAAEVFDKAIEDIHQIQKDAREDNRYQNGEIPAWPIVIARLPKGWGGPR YNDWSGPKFDGKGMPIEHSFRAHQVPLPLSSKNMGTLPEFVKWMTSYQPETLFNADGSLK EELRDFAPKGEMRMASNPVTNGGVDSSNLVLPDWQEFANPISENNRGKLLPDTNDNMDMN VLSKYFAEIVKLNPTRFRLFGPDETMSNRFWEMFKVTNRQWMQVIKNPNDEFISPEGRII DSQLSEHQAEGWLEGYTLTGRTGAFASYESFLRVVDSMLTQHFKWIRQAADQKWRHDYPS LNVISTSTVFQQDHNGYTHQDPGMLTHLAEKKSDFIRQYLPADGNTLLAVFDRAFQDRSK INHIVASKQPRQQWFTKEEAEKLATDGIATIDWASTAKDGEAVDLVFASAGAEPTIETLA ALHLVNEVFPQAKFRYVNVVELGRLQKKKGALNQERELSDEEFEKYFGPSGTPVIFGFHG YEDLIESIFYQRGHDGLIVHGYREDGDITTTYDMRVYSELDRFHQAIDAMQVLYVNRKVN QGLAKAFIDRMKRTLVKHFEVTRNEGVDIPDFTEWVWSDLKK
experiment.sample.molecule[0].mw95.727
experiment.sample.molecule[0].total_mw191.454
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.name20mM potassium phosphate 150mM NaCl 0.007 %(w/v) β-octyl glucoside 1mM DTT 1mM MgCl 1mM thiaminpyrophosphate 2 %(v/v) glycerol
experiment.sample.buffer.concentration_unitnull
experiment.sample.buffer.commentSEC11 buffer
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentrationnull
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph7.0
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodnull
experiment.sample.namePhosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0
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].addressGermany
experiment.contributor[0].affiliation[0].full_nameKiel University
experiment.contributor[0].affiliation[0].webpagehttps://www.uni-kiel.de
experiment.contributor[0].contributor_nameAxel
experiment.contributor[0].contributor_surnameScheidig
experiment.contributor[0].orcidhttps://orcid.org/0000-0002-2382-8818
experiment.concentration_methodnull
experiment.concentration_unitnull
experiment.date2017-09-07
experiment.storage_temperature20.0
experiment.cell_temperature20.0
experiment.exposure_time0.045
experiment.number_of_frames29
experiment.wavelength0.124
experiment.sample_detector_distance3.0
experiment.concentration_minnull
experiment.concentration_max8.0
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.025
experiment.s_max5.064
experiment.total_exposure_timenull
experiment.seccolumnnull
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fits[0].models[0].pdb_link[0].pdb_code6gua
fits[0].models[0].pdb_link[0].ext_code6GUA
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fits[0].models[0].model_mw186.9
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetryP2
fits[0].models[0].commentPDB-ID 6GUA is a tetramer of dimers; the dimer is supposed to be the biological assembly in solution
fits[0].models[0].user366
fits[0].fit_unit1/A
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fits[0].softwareCRYSOL
fits[0].chi_square_value3.244
fits[0].p_value0.0
fits[0].fit_residual_plotpk7_ref82_AB_fitresiduals_img.png
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fits[0].description
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fits[1].chi_square_value1.9
fits[1].p_value0.0
fits[1].fit_residual_plotPKLl2mop-1_fitresiduals_img.png
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fits[1].software_versionnull
fits[1].description
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_version5.0
i0_calibration_standardnull
descriptionnull
experiment_descriptionSynchrotron SAXS data from solutions of phosphoketolase in 20mM potassium phosphate, 150mM NaCl, 0.007 %(w/v) β-octyl glucoside, 1mM DTT, 1mM MgCl2, 1mM thiaminpyrophosphate, 2 % v/v glycerol, pH 7 were collected on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 8.00 mg/ml was measured at 20°C. 29 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.
tags[]
intensity_unit1/cm
experimental_mw164.0
experimental_mw_errornull
guinier_i0_mw146.0
guinier_i0_mw_errornull
porod_mw148.0
porod_mw_errornull
pddf_i021180.0
pddf_i0_errornull
guinier_i021282.0
guinier_i0_error14.3
pddf_rg3.387
pddf_rg_errornull
guinier_rg3.44
guinier_rg_error0.55
pddf_dmax10.15
pddf_dmax_errornull
porod_volume237.0
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first34
guinier_point_last128
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datanull
intensities_log_log_plotSASDEF5_datloglog_img.png
symmetrynull
last_modified2023-06-21T07:56:39.492710+02:00
bragg_peak[]
manifest.json:36 field values
Field pathRaw value
codeSASDEF5
statussuccess
started_at2026-08-11T14:47:00.832243+00:00
finished_at2026-08-11T14:47:12.527052+00:00
source_last_modified2023-06-21T07:56:39.492710+02:00
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View the complete summary.json source
{
  "code": "SASDEF5",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Crystal structure of a xylulose 5-phosphate phosphoketolase. insights into the substrate specificity for xylulose 5-phosphate.",
    "publication": {
      "title": "Crystal structure of a xylulose 5-phosphate phosphoketolase. insights into the substrate specificity for xylulose 5-phosphate.",
      "author_list": "Scheidig AJ, Horvath D, Szedlacsek SE",
      "journal": "J Struct Biol",
      "doi": "10.1016/j.jsb.2019.04.017",
      "pmid": "31059775",
      "published_date": "2019 May 3"
    },
    "status": "released",
    "submitted_date": "2018-09-30",
    "released_date": "2019-05-08"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEF5.dat",
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      "country": "Germany",
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      "type_of_source": "X-ray synchrotron",
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          "long_name": "Probable phosphoketolase",
          "short_name": null,
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          "organism": "Lactococcus lactis subsp. lactis",
          "uniprot_code": "Q9CFH4",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTEYNSEAYLKKLDKWWRAATYLGAGMIFLKENPLFSVTGTPIKAENLKANPIGHWGTVS\nGQTFLYAHANRLINKYDQKMFYMGGPGHGGQAMVVPSYLDGSYTEAYPEITQDLEGMSRL\nFKRFSFPGGIGSHMTAQTPGSLHEGGELGYVLSHATGAILDQPEQIAFAVVGDGEAETGP\nLMTSWHSIKFINPKNDGAILPILDLNGFKISNPTLFARTSDVDIRKFFEGLGYSPRYIEN\nDDIHDYMAYHKLAAEVFDKAIEDIHQIQKDAREDNRYQNGEIPAWPIVIARLPKGWGGPR\nYNDWSGPKFDGKGMPIEHSFRAHQVPLPLSSKNMGTLPEFVKWMTSYQPETLFNADGSLK\nEELRDFAPKGEMRMASNPVTNGGVDSSNLVLPDWQEFANPISENNRGKLLPDTNDNMDMN\nVLSKYFAEIVKLNPTRFRLFGPDETMSNRFWEMFKVTNRQWMQVIKNPNDEFISPEGRII\nDSQLSEHQAEGWLEGYTLTGRTGAFASYESFLRVVDSMLTQHFKWIRQAADQKWRHDYPS\nLNVISTSTVFQQDHNGYTHQDPGMLTHLAEKKSDFIRQYLPADGNTLLAVFDRAFQDRSK\nINHIVASKQPRQQWFTKEEAEKLATDGIATIDWASTAKDGEAVDLVFASAGAEPTIETLA\nALHLVNEVFPQAKFRYVNVVELGRLQKKKGALNQERELSDEEFEKYFGPSGTPVIFGFHG\nYEDLIESIFYQRGHDGLIVHGYREDGDITTTYDMRVYSELDRFHQAIDAMQVLYVNRKVN\nQGLAKAFIDRMKRTLVKHFEVTRNEGVDIPDFTEWVWSDLKK",
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          "number_molecules": 2,
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          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
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        "comment": "SEC11 buffer",
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        "concentration": null,
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        "deuteration": null
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      "purity_method": null,
      "name": "Phosphoketolase (L. lactis) with 1 mM thiaminpyrophosphate and 2% v/v glycerol at pH 7.0",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
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    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Germany",
            "full_name": "Kiel University",
            "webpage": "https://www.uni-kiel.de"
          }
        ],
        "contributor_name": "Axel",
        "contributor_surname": "Scheidig",
        "orcid": "https://orcid.org/0000-0002-2382-8818"
      }
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    "concentration_unit": null,
    "date": "2017-09-07",
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    "cell_temperature": 20.0,
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    "wavelength": 0.124,
    "sample_detector_distance": 3.0,
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              "difference_with_model": "derived"
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          "symmetry": "P2",
          "comment": "PDB-ID 6GUA is a tetramer of dimers; the dimer is supposed to be the biological assembly in solution",
          "user": 366
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/pk7_ref82_AB_fit_img.png",
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  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}
View the complete manifest.json source
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