Designed hollow protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)

{
  "code": "SASDDZ8",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/nm",
  "project": {
    "title": "Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces.",
    "publication": {
      "title": "Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces.",
      "author_list": "Kawakami N, Kondo H, Matsuzawa Y, Hayasaka K, Nasu E, Sasahara K, Arai R, Miyamoto K",
      "journal": "Angew Chem Int Ed Engl",
      "doi": "10.1002/anie.201805565",
      "pmid": "30066354",
      "published_date": "2018 Jul 31"
    },
    "status": "released",
    "submitted_date": "2018-06-24",
    "released_date": "2018-08-03"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDZ8.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDZ8.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ8_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ8_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDZ8_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ8_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDZ8.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Reverse-biased silicon diode array",
        "name": "Pilatus3 1M",
        "resolution": 172.0
      },
      "name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
      "city": "Tsukuba",
      "country": "Japan",
      "beamline_name": "BL-6A",
      "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": "Fusion protein of LSm and MyoX-coil",
          "short_name": "TIP60 protomer",
          "sequence": "MGSSHHHHHHSQDPKNIKIMRLVTGEDIIGNISESQGLITIKKAFVIIPMQATPGKPVQLVLSPWQPYTDDKEIVIDDSKVITITSPKDDIIKSYESHTRVLENKQVEEILRLEKEIEDLQRMKEQQELSLTEASLQKLQERRDQELRRLEEE",
          "organism": "Artificial protein",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "other",
          "molecular_type": "protein",
          "uniprot_sequence": null,
          "mw": 17.766,
          "total_mw": 1065.96,
          "number_molecules": 60,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Designed hollow protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Japan",
            "full_name": "Shinshu University",
            "webpage": "https://www.shinshu-u.ac.jp"
          }
        ],
        "contributor_name": "Ryoichi",
        "contributor_surname": "Arai",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2017-11-11",
    "storage_temperature": null,
    "cell_temperature": 25.0,
    "exposure_time": 5.0,
    "number_of_frames": 30,
    "wavelength": 0.15,
    "sample_detector_distance": 2.023,
    "concentration_min": 0.98,
    "concentration_max": 4.97,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.057,
    "s_max": 2.603,
    "total_exposure_time": null,
    "seccolumn": null
  },
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        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDZ8_fit1_model1_img.png",
          "software": "DAMMIN",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
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          "bead_radius": 8.25,
          "log": null,
          "symmetry": null,
          "comment": null,
          "user": 303
        },
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDZ8_fit1_model2_img.png",
          "software": "DAMFILT",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "dummy",
          "software_version": null,
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          "log": null,
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      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/refine_ws44bWi_fit_img.png",
      "software": "DAMMIN",
      "chi_square_value": 2.976,
      "p_value": 1e-06,
      "fit_residual_plot": "refine_ws44bWi_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDZ8_fit1.fir",
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      "software_version": null,
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  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "5.0",
  "i0_calibration_standard": null,
  "description": "The ab initio dummy atom bead models displayed in this entry are: Top - a refined DAMMIN model and corresponding fit generated from 20 individual model spatial alignments; Bottom - the bead-occupancy and volume-corrected (averaged) spatial representation of TIP60 (DAMFILT) obtained from 20 individual model spatial alignments.",
  "experiment_description": "Synchrotron SAXS data from solutions of a designed hollow protein nanoparticle, TIP60, in 25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol, pH 8 were collected on the BL-6A beam line at the Photon Factory (PF), High Energy Acceleration Reserch Organization (KEK) storage ring (Tsukuba, Japan) using a PILATUS3 1M detector at a sample-detector distance of 2.0 m and at a wavelength of λ = 0.15 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.0 and 5.0 mg/ml were measured at 25°C. 30 successive 5 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. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.",
  "tags": [],
  "intensity_unit": "1/cm",
  "experimental_mw": 1063.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": 1063.0,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": 0.6241,
  "pddf_i0_error": null,
  "guinier_i0": 0.643,
  "guinier_i0_error": 0.001,
  "pddf_rg": 8.952,
  "pddf_rg_error": null,
  "guinier_rg": 9.39,
  "guinier_rg_error": 0.06,
  "pddf_dmax": 23.0,
  "pddf_dmax_error": null,
  "porod_volume": null,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 4,
  "guinier_point_last": 23,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDDZ8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2021-08-18T17:32:55.174589+02:00",
  "bragg_peak": []
}

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