Circadian clock protein KaiC (hydrogenated-KaiC in 100% v/v D₂O ) measured by SEC-SANS

{
  "code": "SASDWF3",
  "status": "Published",
  "type_of_curve": "SEC-SAS",
  "angular_unit": "1/A",
  "project": {
    "title": "Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux",
    "publication": {
      "title": "Size-exclusion chromatography–small-angle neutron scattering system optimized for an instrument with medium neutron flux",
      "author_list": "Morishima K, Inoue R, Nakagawa T, Shimizu M, Sakamoto R, Oda T, Mayumi K, Sugiyama M",
      "journal": "Journal of Applied Crystallography",
      "doi": "10.1107/S1600576725000779",
      "pmid": null,
      "published_date": "2025 Feb 11"
    },
    "status": "released",
    "submitted_date": "2024-12-09",
    "released_date": "2025-02-12"
  },
  "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWF3.out",
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWF3.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWF3_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWF3_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWF3_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWF3_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWF3.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "3He position sensitive detector (PSD)",
        "name": "ORDELA, model 2660N",
        "resolution": 5.0
      },
      "name": "JRR-3 (Japan Atomic Energy Agency)",
      "city": "Ibaraki",
      "country": "Japan",
      "beamline_name": "SANS-U",
      "beam_geometry": null,
      "type_of_source": "neutron source",
      "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": "Circadian clock oscillator protein KaiC",
          "short_name": "kaiC",
          "sequence": "MASWSHPQFEKGATSAEMTSPNNNSEHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHLQIIKSEINDFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFMGAHSITDSHISTITDTIILLQYVEIRGEMSRAINVFKMRGSWHDKAIREFMISDKGPDIKDSFRNFERIISGSPTRITVDEKSELSRIVRGVQEKGPES",
          "organism": "Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)",
          "uniprot_code": "Q79PF4",
          "uniprot_range_first": 2,
          "uniprot_range_last": 519,
          "oligomerization": "hexamer",
          "molecular_type": "protein",
          "uniprot_sequence": "MTSAEMTSPNNNSEHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFL\nYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGG\nFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVM\nTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTIT\nDHGINIFPLGAMRLTQRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLLVSR\nFVENACANKERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPESAGLEDHL\nQIIKSEINDFKPARIAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFM\nGAHSITDSHISTITDTIILLQYVEIRGEMSRAINVFKMRGSWHDKAIREFMISDKGPDIK\nDSFRNFERIISGSPTRITVDEKSELSRIVRGVQEKGPES",
          "mw": 59.329,
          "total_mw": 355.974,
          "number_molecules": 6,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": "The protein construct contains an additional MASWSHPQFEKGA N-terminal extension."
        }
      ],
      "buffer": {
        "name": "50 mM sodium phosphate buffer, 150 mM NaCl, 5 mM MgCl₂, 0.5 mM EDTA, 1 mM ATP, 1 mM DTT, 50 mM arginine, 50 mM glutamine, in 100% D₂O",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 7.8,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Circadian clock protein KaiC (hydrogenated-KaiC in 100% v/v D₂O ) measured by SEC-SANS",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": null,
            "full_name": "Kyoto University",
            "webpage": null
          }
        ],
        "contributor_name": "Ken",
        "contributor_surname": "Morishima",
        "orcid": "https://orcid.org/0000-0003-1091-3850"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2024-07-02",
    "storage_temperature": 10.0,
    "cell_temperature": 25.0,
    "exposure_time": 600.0,
    "number_of_frames": 24,
    "wavelength": 0.6,
    "sample_detector_distance": 4.0,
    "concentration_min": null,
    "concentration_max": 5.6,
    "sample_volume": 0.5,
    "flow_rate": 0.0,
    "s_min": 0.106,
    "s_max": 3.972,
    "total_exposure_time": null,
    "seccolumn": 47
  },
  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": "SEC elution paused during SANS measurements.",
  "experiment_description": "SANS data from solutions of the Circadian clock protein KaiC (hydrogenated-KaiC) in 50 mM sodium phosphate buffer, 150 mM NaCl, 5 mM MgCl₂, 0.5 mM EDTA, 1 mM ATP, 1 mM DTT, 50 mM arginine, 50 mM glutamine, 100% v/v D₂O, pH 7.8 were collected on the SANS-U beam line at JRR-3 (Japan Atomic Energy Agency; Ibaraki, Japan) using a ORDELA, model 2660N detector at a sample-detector distance of 4 and 1.03 m at a wavelength of λ = 0.6 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Stop-flow mode In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 0.50 μl sample at 5.6 mg/ml was injected onto a Cytiva Superdex 200 Increase 10/300 column at 25°C. 24 successive 600 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.",
  "tags": [],
  "intensity_unit": "1/cm",
  "experimental_mw": 334.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": 334.0,
  "guinier_i0_mw_error": 11.0,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": 0.3786,
  "pddf_i0_error": null,
  "guinier_i0": 0.393384,
  "guinier_i0_error": null,
  "pddf_rg": 4.08,
  "pddf_rg_error": null,
  "guinier_rg": 4.37,
  "guinier_rg_error": 0.07,
  "pddf_dmax": 11.91,
  "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": 22,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDWF3_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2025-02-12T13:44:50.284921+01:00",
  "bragg_peak": []
}

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  "status": "success",
  "started_at": "2026-08-11T13:59:27.999614+00:00",
  "finished_at": "2026-08-11T13:59:34.826686+00:00",
  "source_last_modified": "2025-02-12T13:44:50.284921+01:00",
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