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SASDAC2

Lysozyme in sodium acetate

Data type: SASBDB experimental data Status: Published Curve type: Single concentration Last updated: 2023-05-25T11:21:52.654103+02:00
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1. Samples, Components and Experimental Conditions Sample & Experiment

Sample 1 · Lysozyme in sodium acetate

Concentration— – 8.09 mg/mlBuffer / pH40 mM Sodium Acetate / 3.8
Experimental temperature10.0 Facility / beamlineDORIS III, DESY / EMBL X33
Wavelength0.15 nmExposure15.0 s × 8

Molecular Components

ComponentType / organismUniProt and ConstructOligomeric StateMolecular weight
Lysozyme C
View sequence
>SP|P00698|LYSC_CHICKLYSOZYMECOS=GALLUSGALLUSGN=LYZPE=1SV=1MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDVQAWIRGCRL
proteinGallus gallusP00698—–—monomerMolecule count 116.24 kDa

Experimental Curves

CurvePoints / columnsq rangeUncertainty qualityNegative-intensity pointsSource file
12168[3]0.0871252–6.01453 1/nmHas uncertainty columnMissing 05sasbdb/entries/c2/sasdac2/source/SASDAC2.dat
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2. Measurements Reported by SASBDB Reported Results

MetricMethodValueUncertaintyUnit
dmaxP(r)4.0—nm
i0Guinier12.4——
i0P(r)12.0——
mwExperimental11.0—kDa
mwGuinier I(0)11.0—kDa
porod_volumePorod17.2—nm³
rgGuinier1.47—nm
rgP(r)1.43—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 name40 mM Sodium AcetateBuffer concentration40.0 mM
pH3.8Additives—
Buffer description—
Purity measurement methodgel filtrationExtinction coefficient26.53
Absorbance—Scattering contrast3.047
Specific volume / dry volume0.7402 / 19648Mixture / deuteration— / —

Acquisition Conditions and Instrument

Measurement date2012-09-21Storage / measurement temperature10.0 / 10.0
Exposure time15.0Frames8
Wavelength0.15Sample-to-detector distance2.7
SourceX-ray synchrotronDetectorPilatus 1M-W
Facility / beamlineDORIS III, DESY / EMBL X33 · Hamburg, Germany
q range0.087 – 6.015Sample 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
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full_entry_zipsasbdb/entries/c2/sasdac2/source/SASDAC2.zipdownloaded120768e4ea2b946848bd3de600faaf5fa279a2afc82e4ddadd1e2a40a47e294fc0d214DownloadView source fileSource site
pddfsasbdb/entries/c2/sasdac2/source/SASDAC2.outdownloaded36896b745335a59d67647f9cb8f4a5c64f8a051dbbb0bf19fc435761de0260c4cc082DownloadView source fileSource site
sascifsasbdb/entries/c2/sasdac2/source/SASDAC2.sascifdownloaded690378d0c1059b442c32ae1d5b3255a9d0fcdfa4b8bc790a0a709633becc60483feb1fDownloadView source fileSource site
summarysasbdb/entries/c2/sasdac2/source/summary.jsondownloaded7359a51e69dc30e8634159b55cafb7ff9371af11c2adf56ba7fda4cd3411b707fc57DownloadView source fileSource site
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full_entry_zip：source record and ZIP contents (6 items)
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pddf：source record
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sascif：source record
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summary：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：174 field values
Field pathRaw value
codeSASDAC2
statusPublished
type_of_curveSingle concentration
angular_unit1/nm
project.titleStandard proteins
project.publicationnull
project.statusreleased
project.submitted_datenull
project.released_date2015-07-07
pddf_datahttps://www.sasbdb.org/media/p_of_R_files/SASDAC2.out
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intensities_log_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAC2_dat_img.png
intensities_kratky_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAC2_kratky_img.png
pddf_plothttps://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAC2_pofr_img.png
intensities_guinier_plothttps://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAC2_guinier_img.png
sascif_datahttps://www.sasbdb.org/media/sascif/sascif_files/SASDAC2.sascif
experiment.instrument.detector.typeCustom-built
experiment.instrument.detector.namePilatus 1M-W
experiment.instrument.detector.resolution0.172
experiment.instrument.nameDORIS III, DESY
experiment.instrument.cityHamburg
experiment.instrument.countryGermany
experiment.instrument.beamline_nameEMBL X33
experiment.instrument.beam_geometry0.60
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_nameLysozyme C
experiment.sample.molecule[0].short_nameLys
experiment.sample.molecule[0].sequence>sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1 MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG NGMNAWVAWRNRCKGTDVQAWIRGCRL
experiment.sample.molecule[0].organismGallus gallus
experiment.sample.molecule[0].uniprot_codeP00698
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_sequenceMRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA TNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG NGMNAWVAWRNRCKGTDVQAWIRGCRL
experiment.sample.molecule[0].mw16.24
experiment.sample.molecule[0].total_mw14.313
experiment.sample.molecule[0].number_molecules1
experiment.sample.molecule[0].complex_statenull
experiment.sample.molecule[0].deuterationnull
experiment.sample.molecule[0].molecule_sourcebiological
experiment.sample.molecule[0].molecule_descriptionnull
experiment.sample.buffer.name40 mM Sodium Acetate
experiment.sample.buffer.concentration_unitmM
experiment.sample.buffer.commentnull
experiment.sample.buffer.additivenull
experiment.sample.buffer.concentration40.0
experiment.sample.buffer.pkanull
experiment.sample.buffer.ph3.8
experiment.sample.buffer.deuterationnull
experiment.sample.purity_methodgel filtration
experiment.sample.nameLysozyme in sodium acetate
experiment.sample.ext_coefficient26.53
experiment.sample.contrast3.047
experiment.sample.specific_vol0.7402
experiment.sample.dry_vol19648
experiment.sample.absorbptionnull
experiment.sample.deuterationnull
experiment.sample.mixturenull
experiment.contributor[0].affiliation[0].short_nameEMBL-Hamburg
experiment.contributor[0].affiliation[0].addressNotkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany
experiment.contributor[0].affiliation[0].full_nameEuropean Molecular Biology Laboratory (EMBL) - Hamburg outstation
experiment.contributor[0].affiliation[0].webpagehttp://www.embl-hamburg.de/index.php
experiment.contributor[0].contributor_nameDarja
experiment.contributor[0].contributor_surnameRuskule
experiment.contributor[0].orcidnull
experiment.concentration_methodnanodrop
experiment.concentration_unitmg/ml
experiment.date2012-09-21
experiment.storage_temperature10.0
experiment.cell_temperature10.0
experiment.exposure_time15.0
experiment.number_of_frames8
experiment.wavelength0.15
experiment.sample_detector_distance2.7
experiment.concentration_minnull
experiment.concentration_max8.09
experiment.sample_volumenull
experiment.flow_ratenull
experiment.s_min0.087
experiment.s_max6.015
experiment.total_exposure_timenull
experiment.seccolumnnull
fits[0].models[0].model_plothttps://www.sasbdb.org/media/pdb_file/images/SASDAC2_fit1_model1_img.png
fits[0].models[0].softwareCRYSOL
fits[0].models[0].pdb_link[]
fits[0].models[0].model_titlenull
fits[0].models[0].type_of_modelatomic
fits[0].models[0].software_version
fits[0].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDAC2_fit1_model1.pdb
fits[0].models[0].model_mw14.32
fits[0].models[0].bead_radiusnull
fits[0].models[0].lognull
fits[0].models[0].symmetry
fits[0].models[0].comment
fits[0].models[0].user1
fits[0].fit_unit1/A
fits[0].fit_plothttps://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAC2_fit1_fixed_fit_img.png
fits[0].softwarenull
fits[0].chi_square_value1.452025
fits[0].p_value0.0
fits[0].fit_residual_plotSASDAC2_fit1_fitresiduals_img.png
fits[0].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDAC2_fit1.fit
fits[0].fit_lognull
fits[0].software_versionnull
fits[0].descriptionnull
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fits[1].models[0].softwareDAMMIF
fits[1].models[0].pdb_link[]
fits[1].models[0].model_titlenull
fits[1].models[0].type_of_modeldummy
fits[1].models[0].software_version
fits[1].models[0].model_datahttps://www.sasbdb.org/media/pdb_file/SASDAC2_fit2_model1.pdb
fits[1].models[0].model_mw10.35
fits[1].models[0].bead_radius1.0
fits[1].models[0].loghttps://www.sasbdb.org/media/log_files/lys_orig_2.log
fits[1].models[0].symmetry
fits[1].models[0].comment
fits[1].models[0].user1
fits[1].fit_unit1/A
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fits[1].softwarenull
fits[1].chi_square_value2.873025
fits[1].p_value0.0
fits[1].fit_residual_plotSASDAC2_fit2_fitresiduals_img.png
fits[1].fit_datahttps://www.sasbdb.org/media/fitting_files/SASDAC2_fit2.fir
fits[1].fit_lognull
fits[1].software_versionnull
fits[1].descriptionnull
estimated_volume_methodnull
pddf_softwareATSAS GNOM
pddf_software_versionGNOM
i0_calibration_standardBSA
descriptionnull
experiment_descriptionnull
tags[0]X33
intensity_unitnull
experimental_mw11.0
experimental_mw_errornull
guinier_i0_mw11.0
guinier_i0_mw_errornull
porod_mwnull
porod_mw_errornull
pddf_i012.0
pddf_i0_errornull
guinier_i012.4
guinier_i0_errornull
pddf_rg1.43
pddf_rg_errornull
guinier_rg1.47
guinier_rg_errornull
pddf_dmax4.0
pddf_dmax_errornull
porod_volume17.2
porod_volume_errornull
estimated_volumenull
estimated_volume_errornull
guinier_point_first189
guinier_point_last294
pddf_point_firstnull
pddf_point_lastnull
i0_calibration_standard_datahttps://www.sasbdb.org/media/standard_curves/bsa_203_1.dat
intensities_log_log_plotSASDAC2_datloglog_img.png
symmetrynull
last_modified2023-05-25T11:21:52.654103+02:00
bragg_peak[]
manifest.json：36 field values
Field pathRaw value
codeSASDAC2
statussuccess
started_at2026-08-11T13:35:10.197188+00:00
finished_at2026-08-11T13:35:24.261435+00:00
source_last_modified2023-05-25T11:21:52.654103+02:00
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View the complete summary.json source
{
  "code": "SASDAC2",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "Standard proteins",
    "publication": null,
    "status": "released",
    "submitted_date": null,
    "released_date": "2015-07-07"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAC2.dat",
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  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAC2_pofr_img.png",
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  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAC2.sascif",
  "experiment": {
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        "name": "Pilatus 1M-W",
        "resolution": 0.172
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      "name": "DORIS III, DESY",
      "city": "Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL X33",
      "beam_geometry": "0.60",
      "type_of_source": "X-ray synchrotron",
      "point_source": null,
      "line_collimation": null,
      "sample_path_length": null,
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      "line_collimation_integrationwidth": null,
      "xray_energy": null,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Lysozyme C",
          "short_name": "Lys",
          "sequence": ">sp|P00698|LYSC_CHICK Lysozyme C OS=Gallus gallus GN=LYZ PE=1 SV=1\nMRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA\nTNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG\nNGMNAWVAWRNRCKGTDVQAWIRGCRL\n\n",
          "organism": "Gallus gallus",
          "uniprot_code": "P00698",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA\nTNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG\nNGMNAWVAWRNRCKGTDVQAWIRGCRL",
          "mw": 16.24,
          "total_mw": 14.313,
          "number_molecules": 1,
          "complex_state": null,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
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        "concentration_unit": "mM",
        "comment": null,
        "additive": null,
        "concentration": 40.0,
        "pka": null,
        "ph": 3.8,
        "deuteration": null
      },
      "purity_method": "gel filtration",
      "name": "Lysozyme in sodium acetate",
      "ext_coefficient": 26.53,
      "contrast": 3.047,
      "specific_vol": 0.7402,
      "dry_vol": 19648,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
          }
        ],
        "contributor_name": "Darja",
        "contributor_surname": "Ruskule",
        "orcid": null
      }
    ],
    "concentration_method": "nanodrop",
    "concentration_unit": "mg/ml",
    "date": "2012-09-21",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 15.0,
    "number_of_frames": 8,
    "wavelength": 0.15,
    "sample_detector_distance": 2.7,
    "concentration_min": null,
    "concentration_max": 8.09,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.087,
    "s_max": 6.015,
    "total_exposure_time": null,
    "seccolumn": null
  },
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