Glucose isomerase (WAXS)

{
  "code": "SASDCJ8",
  "status": "Published",
  "type_of_curve": "Merged",
  "angular_unit": "1/nm",
  "project": {
    "title": "WAXS benchmark on standard proteins",
    "publication": null,
    "status": "released",
    "submitted_date": "2017-10-17",
    "released_date": "2021-09-13"
  },
  "pddf_data": null,
  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCJ8.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ8_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ8_kratky_img.png",
  "pddf_plot": null,
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCJ8_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCJ8.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": null,
        "name": "Pilatus 2M",
        "resolution": null
      },
      "name": "PETRA III",
      "city": "DESY; Hamburg",
      "country": "Germany",
      "beamline_name": "EMBL P12",
      "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": "Xylose isomerase",
          "short_name": "GI",
          "sequence": "NYQPTPEDRFTFGLWTVGWEGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDD\r\nTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEA\r\nFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKL\r\nFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFR\r\nADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGARG",
          "organism": "Streptomyces rubiginosus",
          "uniprot_code": "P24300",
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "tetramer",
          "molecular_type": "protein",
          "uniprot_sequence": "MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIP\nFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTI\nRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAI\nEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK\nLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW\nASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEF\nDVDAAAARGMAFERLDQLAMDHLLGARG",
          "mw": 43.097,
          "total_mw": 172.388,
          "number_molecules": 4,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "100 mM tris pH 8.0, 100 mM NaCl, 1 mM MgCl2",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 8.0,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Glucose isomerase (WAXS)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": "EMBL-Hamburg",
            "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany",
            "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation",
            "webpage": "http://www.embl-hamburg.de/index.php"
          }
        ],
        "contributor_name": "Maxim",
        "contributor_surname": "Petoukhov",
        "orcid": null
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2016-10-17",
    "storage_temperature": 10.0,
    "cell_temperature": 10.0,
    "exposure_time": 0.2,
    "number_of_frames": null,
    "wavelength": 0.062,
    "sample_detector_distance": null,
    "concentration_min": 3.6,
    "concentration_max": 14.5,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.099,
    "s_max": 18.005,
    "total_exposure_time": null,
    "seccolumn": null
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          "software": "PDB (Protein Data Bank)",
          "pdb_link": [
            {
              "pdb_code": "1oad",
              "ext_code": "1OAD",
              "ext_type": "pdb",
              "difference_with_model": "identical"
            }
          ],
          "model_title": null,
          "type_of_model": "atomic",
          "software_version": "",
          "model_data": "https://www.sasbdb.org/media/pdb_file/1oadm.pdb",
          "model_mw": 173.7,
          "bead_radius": 1.9,
          "log": null,
          "symmetry": "",
          "comment": "",
          "user": 102
        }
      ],
      "fit_unit": "1/A",
      "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCJ8_fit1_fixed_fit_img.png",
      "software": "CRYSOL",
      "chi_square_value": 29.49,
      "p_value": 0.0,
      "fit_residual_plot": "SASDCJ8_fit1_fitresiduals_img.png",
      "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCJ8_fit1.fit",
      "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/1oad04.log",
      "software_version": "crysol 3.0",
      "description": null
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  ],
  "estimated_volume_method": null,
  "pddf_software": null,
  "pddf_software_version": null,
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of glucose isomerase (a.k.a. xylose isomerase) in 100 mM Tris, 100 mM NaCl, 1 mM MgCl2, pH 8 were collected on the EMBL-P12 beam line at the PETRA III storage ring  (Hamburg, Germany) using a Pilatus 2M detector at a wavelength of λ = 0.062 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 3.6 and 14.5 mg/ml were measured at 10°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.",
  "tags": [
    "benchmark"
  ],
  "intensity_unit": "arbitrary",
  "experimental_mw": 151.0,
  "experimental_mw_error": null,
  "guinier_i0_mw": null,
  "guinier_i0_mw_error": null,
  "porod_mw": null,
  "porod_mw_error": null,
  "pddf_i0": null,
  "pddf_i0_error": null,
  "guinier_i0": 7954.08,
  "guinier_i0_error": 12.5,
  "pddf_rg": null,
  "pddf_rg_error": null,
  "guinier_rg": 3.23,
  "guinier_rg_error": 0.05,
  "pddf_dmax": null,
  "pddf_dmax_error": null,
  "porod_volume": null,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 5,
  "guinier_point_last": 25,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDCJ8_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2023-06-21T07:56:39.492710+02:00",
  "bragg_peak": []
}

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  "started_at": "2026-08-11T15:54:15.763099+00:00",
  "finished_at": "2026-08-11T15:54:24.049528+00:00",
  "source_last_modified": "2023-06-21T07:56:39.492710+02:00",
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