The neutrophil cytosol factor 1 (p47phox) subunit of phagocyte NADPH oxidase

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  "code": "SASDEK3",
  "status": "Published",
  "type_of_curve": "Extrapolated to infinite dilution",
  "angular_unit": "1/A",
  "project": {
    "title": "Quantitative live-cell imaging and 3D modeling reveal critical functional features in the cytosolic complex of phagocyte NADPH oxidase.",
    "publication": {
      "title": "Quantitative live-cell imaging and 3D modeling reveal critical functional features in the cytosolic complex of phagocyte NADPH oxidase.",
      "author_list": "Ziegler CS, Bouchab L, Tramier M, Durand D, Fieschi F, Dupré-Crochet S, Mérola F, Nüße O, Erard M",
      "journal": "J Biol Chem",
      "doi": "10.1074/jbc.RA118.006864",
      "pmid": "30630949",
      "published_date": "2019 Jan 10"
    },
    "status": "released",
    "submitted_date": "2018-08-28",
    "released_date": "2019-01-16"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEK3.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK3_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK3_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEK3_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEK3_guinier_img.png",
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  "experiment": {
    "instrument": {
      "detector": {
        "type": "CCD",
        "name": "AVIEX PCCD170170",
        "resolution": null
      },
      "name": "SOLEIL",
      "city": "Saint-Aubin",
      "country": "France",
      "beamline_name": "SWING",
      "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,
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      "beam_profile_al": null
    },
    "sample": {
      "molecule": [
        {
          "long_name": "Neutrophil cytosol factor 1",
          "short_name": "p47phox",
          "sequence": "GPLGSPNSARMGDTFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEF\r\nHKTLKEMFPIEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLMSLPTKISR\r\nCPHLLDFFKVRPDDLKLPTDNQTKKPETYLMPKDGKSTATDITGPIILQTYRAIADYEKT\r\nSGSEMALSTGDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEP\r\nYVAIKAYTAVEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKSGQDVSQA\r\nQRQIKRGAPPRRSSIRNAHSIHQRSRKRLSQDAYRRNSVRFLQQRRRQARPGPQSPGSPL\r\nEEERQTQRSKPQPAVPPRPSADLILNRCSESTKRKLASAVCGRIVTD",
          "organism": "Homo sapiens",
          "uniprot_code": "P14598",
          "uniprot_range_first": 1,
          "uniprot_range_last": 390,
          "oligomerization": "monomer",
          "molecular_type": "protein",
          "uniprot_sequence": "MGDTFIRHIALLGFEKRFVPSQHYVYMFLVKWQDLSEKVVYRRFTEIYEFHKTLKEMFPI\nEAGAINPENRIIPHLPAPKWFDGQRAAENRQGTLTEYCSTLMSLPTKISRCPHLLDFFKV\nRPDDLKLPTDNQTKKPETYLMPKDGKSTATDITGPIILQTYRAIANYEKTSGSEMALSTG\nDVVEVVEKSESGWWFCQMKAKRGWIPASFLEPLDSPDETEDPEPNYAGEPYVAIKAYTAV\nEGDEVSLLEGEAVEVIHKLLDGWWVIRKDDVTGYFPSMYLQKSGQDVSQAQRQIKRGAPP\nRRSSIRNAHSIHQRSRKRLSQDAYRRNSVRFLQQRRRQARPGPQSPGSPLEEERQTQRSK\nPQPAVPPRPSADLILNRCSESTKRKLASAV",
          "mw": 46.364,
          "total_mw": 46.364,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "50 mM HEPES, 100 mM NaCl, 1 mM EDTA, 2 mM DTT, 5% glycerol",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.5,
        "deuteration": null
      },
      "purity_method": null,
      "name": "The neutrophil cytosol factor 1 (p47phox) subunit of phagocyte NADPH oxidase",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Paris, France",
            "full_name": "I2BC-CNRS",
            "webpage": "http://www.i2bc.paris-saclay.fr"
          }
        ],
        "contributor_name": "Dominique",
        "contributor_surname": "DURAND",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2008-04-23",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 2.0,
    "number_of_frames": 20,
    "wavelength": 0.1,
    "sample_detector_distance": 1.783,
    "concentration_min": 1.0,
    "concentration_max": 4.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.104,
    "s_max": 5.004,
    "total_exposure_time": null,
    "seccolumn": null
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      "models": [
        {
          "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEK3_fit1_model1_img.png",
          "software": "Custom in-house",
          "pdb_link": [],
          "model_title": null,
          "type_of_model": "atomic",
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          "comment": null,
          "user": 262
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      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/p47_Model00_fit_img.png",
      "software": "BUNCH",
      "chi_square_value": 1.245,
      "p_value": 0.0,
      "fit_residual_plot": "fit4columns1677_fitresiduals_img.png",
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      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/p47_Model00.log",
      "software_version": "08",
      "description": "p47phox in solution: \r\nComparison of the experimental data (blue dots) with the calculated scattering pattern (red line) of the BUNCH model shown on the right chi2=1.245. The ultimate adjustment shown here was performed using the program CRYSOL."
    }
  ],
  "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 p47phox subunit of phagocyte NADPH oxidase in 50 mM HEPES 50, 100 mM NaCl, 1 mM EDTA, 2 mM DTT, 5% glycerol, pH 7.5 were collected on the SWING beam line SOLEIL (Saint-Aubin, France) using a CCD AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Samples were studied at different concentrations ranging from 1.0 to 4.0 mg/ml measured at 10°C. 20 successive 2 second frames were collected. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program package PRIMUS. Intensities were put on an absolute scale (cm-1) using water scattering. The final pattern used for fitting was obtained by extrapolating to infinite dilution of the set of curves recorded at the different concentrations.  Molecular mass was obtained using the bayesian inference approach proposed in PRIMUS/qt, which combines four concentration independent MM estimators: M=47.7 kDa within the credibility interval [45.2-50.3].",
  "tags": [],
  "intensity_unit": "1/cm",
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  "experimental_mw_error": null,
  "guinier_i0_mw": 44.1,
  "guinier_i0_mw_error": 4.0,
  "porod_mw": 51.1,
  "porod_mw_error": null,
  "pddf_i0": 0.03307,
  "pddf_i0_error": 0.0003,
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  "guinier_i0_error": 0.0003,
  "pddf_rg": 3.32,
  "pddf_rg_error": 0.03,
  "guinier_rg": 3.17,
  "guinier_rg_error": 0.03,
  "pddf_dmax": 12.5,
  "pddf_dmax_error": 1.0,
  "porod_volume": 76.7,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 7,
  "guinier_point_last": 66,
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  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
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