Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 8mer hairpin dsRNA (SEC-peak2)

{
  "code": "SASDBQ8",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/A",
  "project": {
    "title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.",
    "publication": {
      "title": "Combined roles of ATP and small hairpin RNA in the activation of RIG-I revealed by solution-based analysis.",
      "author_list": "Shah N, Beckham SA, Wilce JA, Wilce MCJ",
      "journal": "Nucleic Acids Res",
      "doi": "10.1093/nar/gkx1307",
      "pmid": "29346611",
      "published_date": "2018 Apr 6"
    },
    "status": "released",
    "submitted_date": "2016-12-11",
    "released_date": "2018-01-22"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBQ8.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBQ8.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBQ8_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBQ8_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBQ8_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBQ8_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBQ8.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "Australian  Synchrotron",
      "city": "Melbourne",
      "country": "Australia",
      "beamline_name": "SAXS/WAXS",
      "beam_geometry": "Point",
      "type_of_source": "X-ray synchrotron",
      "point_source": true,
      "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": "Probable ATP-dependent RNA helicase DDX58",
          "short_name": "RIG-I",
          "sequence": "MHHHHHHTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERNKFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK",
          "organism": "Homo sapiens",
          "uniprot_code": "O95786",
          "uniprot_range_first": 1,
          "uniprot_range_last": 925,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKF\nLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIP\nTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERN\nKFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSP\nFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQI\nPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI\nPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNT\nDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMR\nDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFL\nYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESV\nSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGI\nLTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN\nVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKI\nLHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKE\nCFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATG\nVQTLYSKWKDFHFEKIPFDPAEMSK",
          "mw": 107.421,
          "total_mw": 214.842,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "5´ppp 8mer hairpin dsRNA",
          "short_name": "8bp",
          "sequence": "GGCGCGGCUUCGGCCGCGCC",
          "organism": null,
          "uniprot_code": null,
          "uniprot_range_first": 1,
          "uniprot_range_last": 20,
          "oligomerization": "dimer",
          "molecular_type": "RNA",
          "uniprot_sequence": null,
          "mw": 6.484,
          "total_mw": 12.968,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.4,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 8mer hairpin dsRNA (SEC-peak2)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Melbourne, Australia",
            "full_name": "Monash University",
            "webpage": "http://www.monash.edu/"
          }
        ],
        "contributor_name": "Neelam",
        "contributor_surname": "Shah",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-11-20",
    "storage_temperature": 4.0,
    "cell_temperature": 15.0,
    "exposure_time": 2.0,
    "number_of_frames": 17,
    "wavelength": 0.10332,
    "sample_detector_distance": 1.6,
    "concentration_min": null,
    "concentration_max": null,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.103,
    "s_max": 2.498,
    "total_exposure_time": null,
    "seccolumn": null
  },
  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "GNOM v4.5",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Probable ATP-dependent RNA helicase DDX58 (Full-length RIG-I) plus 8mer hairpin dsRNA (SEC-peak2) in 25 mM HEPES, 150 mM NaCl, 2.5 mM MgCl2, 10% glycerol and 1mM DTT, pH 7.4 were collected using size exclusion chromatography (SEC-SAXS) on the SAXS/WAXS camera on the storage ring Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 1.6 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle). Data frames (17 x 2 s exposures) were collected through the SEC elution peak at 27.8 min (GE Healthcare Life Sciences Superdex 200 10/300; 0.4 ml/min; 100 μl injection at 8 mg/ml). The data were normalized to the intensity of the transmitted beam and radially averaged; the radially averaged scattering of the solvent-blank was subtracted and the different curves were scaled to yield the final composite scattering curve. The SAXS data were collected at 15 °C.",
  "tags": [],
  "intensity_unit": null,
  "experimental_mw": 228.4,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": 232.8,
  "porod_mw_error": null,
  "pddf_i0": 0.0193,
  "pddf_i0_error": null,
  "guinier_i0": 0.0189,
  "guinier_i0_error": null,
  "pddf_rg": 60.2,
  "pddf_rg_error": null,
  "guinier_rg": 5.71,
  "guinier_rg_error": null,
  "pddf_dmax": 24.55,
  "pddf_dmax_error": null,
  "porod_volume": 388.55,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 6,
  "guinier_point_last": 28,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDBQ8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2019-12-06T13:07:15.624532+01:00",
  "bragg_peak": []
}

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