Lysozyme (WAXS)

{
  "code": "SASDCK8",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "WAXS benchmark on standard proteins",
    "publication": null,
    "status": "released",
    "submitted_date": "2017-10-17",
    "released_date": "2021-09-13"
  },
  "pddf_data": null,
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCK8.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK8_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK8_kratky_img.png",
  "pddf_plot": null,
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK8_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCK8.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "beam_geometry": null,
      "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": "Lysozyme C",
          "short_name": "Lysozyme, lys",
          "sequence": "KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA\r\nTNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG\r\nNGMNAWVAWRNRCKGTDVQAWIRGCRL",
          "organism": "Gallus gallus",
          "uniprot_code": "P00698",
          "uniprot_range_first": 19,
          "uniprot_range_last": 147,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MRSLLILVLCFLPLAALGKVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQA\nTNRNTDGSTDYGILQINSRWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDG\nNGMNAWVAWRNRCKGTDVQAWIRGCRL",
          "mw": 14.31,
          "total_mw": 14.31,
          "number_molecules": 1,
          "complex_state": null,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": ""
        }
      ],
      "buffer": {
        "name": "40 mM Sodium Acetate pH 4.0, 50 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 4.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Lysozyme (WAXS)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "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": "Maxim",
        "contributor_surname": "Petoukhov",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-05-31",
    "storage_temperature": 20.0,
    "cell_temperature": 20.0,
    "exposure_time": 0.1,
    "number_of_frames": null,
    "wavelength": 0.062,
    "sample_detector_distance": 1.5,
    "concentration_min": 19.4,
    "concentration_max": 25.1,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.242,
    "s_max": 17.856,
    "total_exposure_time": null,
    "seccolumn": null
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    {
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCK8_fit1_model1_img.png",
          "software": "PDB (Protein Data Bank)",
          "pdb_link": [
            {
              "pdb_code": "6lyz",
              "ext_code": "6LYZ",
              "ext_type": "pdb",
              "difference_with_model": "identical"
            }
          ],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": "",
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDCK8_fit1_model1.pdb",
          "model_mw": 14.32,
          "bead_radius": 1.9,
          "log": null,
          "symmetry": "",
          "comment": "",
          "user": 102
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK8_fit1_fixed_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 2.05,
      "p_value": 0.0,
      "fit_residual_plot": "SASDCK8_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCK8_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/6lyz04.log",
      "software_version": "crysol 3.0",
      "description": null
    }
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  "estimated_volume_method": null,
  "pddf_software": null,
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of lysozyme in 40 mM sodium acetate, 50 mM NaCl, pH 4 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 1.5 m and at a wavelength of λ = 0.062 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 19.4 and 25.1 mg/ml were measured at 20°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the data scaled to protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
  "tags": [
    "benchmark"
  ],
  "intensity_unit": "arbitrary",
  "experimental_mw": 12.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": null,
  "pddf_i0_error": null,
  "guinier_i0": 648.36,
  "guinier_i0_error": 0.93,
  "pddf_rg": null,
  "pddf_rg_error": null,
  "guinier_rg": 1.41,
  "guinier_rg_error": 0.03,
  "pddf_dmax": null,
  "pddf_dmax_error": null,
  "porod_volume": null,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 1,
  "guinier_point_last": 58,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDCK8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}

{
  "code": "SASDCK8",
  "status": "success",
  "started_at": "2026-08-11T15:54:56.596019+00:00",
  "finished_at": "2026-08-11T15:55:03.503488+00:00",
  "source_last_modified": "2023-06-21T07:56:39.492710+02:00",
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