C-terminal truncated bank vole prion protein (amino acids 90-231) bound to Cu(II)

{
  "code": "SASDEX7",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/nm",
  "project": {
    "title": "Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain",
    "publication": {
      "title": "Deciphering Copper Coordination in the Mammalian Prion Protein Amyloidogenic Domain",
      "author_list": "Salzano G, Brennich M, Mancini G, Tran T, Legname G, D’Angelo P, Giachin G",
      "journal": "Biophysical Journal",
      "doi": "10.1016/j.bpj.2019.12.025",
      "pmid": null,
      "published_date": "2020 Jan"
    },
    "status": "released",
    "submitted_date": "2018-11-13",
    "released_date": "2019-11-25"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEX7.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEX7.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX7_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX7_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEX7_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX7_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEX7.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": "Major prion protein",
          "short_name": null,
          "sequence": "GQGGGTHNQWNKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYYEGRSS",
          "organism": "Myodes glareolus",
          "uniprot_code": "Q8VHV5",
          "uniprot_range_first": 90,
          "uniprot_range_last": 231,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MANLSYWLLAFFVTTWTDVGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGTWGQP\nHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHNQWNKPSKPKTNMKHVAGAAAAGA\nVVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCV\nNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQYQKESQAYYEGRSSRAVLLFSSP\nPVILLISF",
          "mw": 16.14,
          "total_mw": 16.14,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "25 mM Ammonium Acetate, 250 mM NaCl, 0.001 mM CuSO4",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 5.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "C-terminal truncated bank vole prion protein (amino acids 90-231) bound to Cu(II)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "ESRF",
            "address": "Grenoble, France",
            "full_name": "European Synchrotron Radiation Facility",
            "webpage": "http://www.esrf.eu/"
          }
        ],
        "contributor_name": "Gabriele",
        "contributor_surname": "Giachin",
        "orcid": "https://orcid.org/0000-0001-7550-0307"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2018-02-25",
    "storage_temperature": 20.0,
    "cell_temperature": 20.0,
    "exposure_time": 1.0,
    "number_of_frames": 1,
    "wavelength": 0.099,
    "sample_detector_distance": 2.864,
    "concentration_min": null,
    "concentration_max": 10.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.108,
    "s_max": 4.928,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [
    {
      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEX7_fit1_model1_img.png",
          "software": "EOM/RANCH",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "mix",
          "software_version": null,
          "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEX7_fit1_model1.pdb",
          "model_mw": 16.02,
          "bead_radius": null,
          "log": "https://www.sasbdb.org/media/log_files/logFile_001_1_SEsHkXF.log",
          "symmetry": "P1",
          "comment": null,
          "user": 388
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEX7_fit1_fixed_fit_img.png",
      "software": "EOM/GAJOE",
      "chi_square_value": 1.275,
      "p_value": 0.215624,
      "fit_residual_plot": "SASDEX7_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEX7_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_L9O40cH.log",
      "software_version": null,
      "description": ""
    }
  ],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of the C-terminal truncated bank vole prion protein (amino acids 90-231) bound to Cu(II) iin 25 mM ammonium acetate, 250 mM NaCl, 0.001 mM CuSO4, pH 5.5 were collected using size exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20 °C using the following parameters: Column type, Superdex 75 10/300 GL (GE Healthcare); Flow rate: 0.5 mL/min; Total acquisition time: 50 min; Injection concentration: 10 mg/mL; Injection volume: 250 μL. The data obtained through the sample elution peak (1963-2030 1 s frames) were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.",
  "tags": [],
  "intensity_unit": "arbitrary",
  "experimental_mw": 16.3,
  "experimental_mw_error": null,
  "guinier_i0_mw": 15.3,
  "guinier_i0_mw_error": null,
  "porod_mw": 15.065,
  "porod_mw_error": null,
  "pddf_i0": 22.36,
  "pddf_i0_error": null,
  "guinier_i0": 21.67,
  "guinier_i0_error": 0.07,
  "pddf_rg": 2.396,
  "pddf_rg_error": null,
  "guinier_rg": 2.2,
  "guinier_rg_error": 0.01,
  "pddf_dmax": 8.7,
  "pddf_dmax_error": null,
  "porod_volume": 30.13,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 54,
  "guinier_point_last": 106,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDEX7_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2020-08-28T15:28:09.860259+02:00",
  "bragg_peak": []
}

{
  "code": "SASDEX7",
  "status": "success",
  "started_at": "2026-08-11T15:41:49.808384+00:00",
  "finished_at": "2026-08-11T15:42:00.388159+00:00",
  "source_last_modified": "2020-08-28T15:28:09.860259+02:00",
  "files": [
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/rest-api/entry/summary/SASDEX7/",
      "path": "/data/saxsdb/sasbdb/entries/x7/sasdex7/source/summary.json",
      "size": 7851,
      "sha256": "e04e09f7a93789f5bbbb9f0e8de8d2f6b5c34d2a23c3bd715d48820d4f180652"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/intensities_files/SASDEX7.dat",
      "path": "/data/saxsdb/sasbdb/entries/x7/sasdex7/source/SASDEX7.dat",
      "size": 51791,
      "sha256": "804640f41ddba35b92a2e0c7c9abd4b47f727370754d1c92add3c0134c8a517e",
      "role": "curve"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/p_of_R_files/SASDEX7.out",
      "path": "/data/saxsdb/sasbdb/entries/x7/sasdex7/source/SASDEX7.out",
      "size": 65545,
      "sha256": "d3326586f46a1e8718a87ba5d256d8fc7d45c3a825f5da2a5232250400a2f03b",
      "role": "pddf"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEX7.sascif",
      "path": "/data/saxsdb/sasbdb/entries/x7/sasdex7/source/SASDEX7.sascif",
      "size": 213191,
      "sha256": "11ecac4abb716b329f148ecf401d63978aaab84c1ce49d2a983e5ea9051d003f",
      "role": "sascif"
    },
    {
      "status": "downloaded",
      "url": "https://www.sasbdb.org/media/zip_directories/SASDEX7.zip",
      "path": "/data/saxsdb/sasbdb/entries/x7/sasdex7/source/SASDEX7.zip",
      "size": 60592,
      "sha256": "0ef7a16126b3e40bb5c5961eb153f73f10ce9e5c4104796e98a65fecb324ea7b",
      "role": "full_entry_zip",
      "zip_member_count": 5,
      "zip_validation": "central_directory_readable"
    }
  ]
}