Pyrococcus furiosus Box C/D sRNP reconstituted with st-sR6 sRNA bound to substrate D (SAXS data)

{
  "code": "SASDGA3",
  "status": "Published",
  "type_of_curve": "Single concentration",
  "angular_unit": "1/nm",
  "project": {
    "title": "The guide sRNA sequence determines the activity level of box C/D RNPs.",
    "publication": {
      "title": "The guide sRNA sequence determines the activity level of box C/D RNPs.",
      "author_list": "Graziadei A, Gabel F, Kirkpatrick J, Carlomagno T",
      "journal": "Elife",
      "doi": "10.7554/eLife.50027",
      "pmid": "32202498",
      "published_date": "2020 Mar 23"
    },
    "status": "released",
    "submitted_date": "2019-07-29",
    "released_date": "2020-03-25"
  },
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  "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDGA3.dat",
  "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA3_dat_img.png",
  "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA3_kratky_img.png",
  "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGA3_pofr_img.png",
  "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGA3_guinier_img.png",
  "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDGA3.sascif",
  "experiment": {
    "instrument": {
      "detector": {
        "type": "Dectris",
        "name": "Pilatus 1M",
        "resolution": 172.0
      },
      "name": "ESRF",
      "city": "Grenoble",
      "country": "France",
      "beamline_name": "BM29",
      "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,
      "beam_profile_ah": null,
      "beam_profile_al": null
    },
    "sample": {
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        {
          "long_name": "Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase",
          "short_name": "Fibrillarin",
          "sequence": ">sp|Q8U4M2|FLPA_PYRFU Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 GN=flpA PE=1 SV=1\r\nMVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGA\r\nAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEE\r\nRRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKS\r\nRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP",
          "organism": "Pyrococcus furiosus",
          "uniprot_code": "Q8U4M2",
          "uniprot_range_first": 1,
          "uniprot_range_last": 227,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MVEVKKHKFPGVYVVIDDDGSEKIATKNLVPGQRVYGERVIKWEGEEYRIWNPHRSKLGA\nAIVNGLKNFPIKPGKSVLYLGIASGTTASHVSDIVGWEGKIYGIEFSPRVLRELVPIVEE\nRRNIIPILGDATKPEEYRALVTKVDVIFEDVAQPTQAKILIDNAKAYLKRGGYGMIAVKS\nRSIDVTKEPEQVFKEVERELSEYFEVIERLNLEPYEKDHALFVVRKP",
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          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
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        },
        {
          "long_name": "50S ribosomal protein L7Ae",
          "short_name": "L7Ae",
          "sequence": ">sp|Q8U160|RL7A_PYRFU 50S ribosomal protein L7Ae OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 GN=rpl7ae PE=1 SV=2\r\nMAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPE\r\nEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKE\r\nLMK",
          "organism": "Pyrococcus furiosus",
          "uniprot_code": "Q8U160",
          "uniprot_range_first": 1,
          "uniprot_range_last": 123,
          "oligomerization": "dimer",
          "molecular_type": "protein",
          "uniprot_sequence": "MAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPE\nEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVKE\nLMK",
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          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "NOP5/NOP56 related protein",
          "short_name": "Nop5",
          "sequence": ">tr|Q8U4M1|Q8U4M1_PYRFU NOP5/NOP56 related protein OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) OX=186497 GN=PF0060 PE=1 SV=1\r\nMKAFISENVRGIYAFDENGNLIEKRYFTDKPEKVLDQLLKGEITKDLEELLNSLKEKGYD\r\nEFVFEHPELSRRAKELGFSATTEFPNIAGERLRSNPEEFLGENWFEEYYKVGVALTRMRI\r\nQEQSGARDKMVIQAIEALDDVDKVINLLVARLREWYSLHFPELDELLPKHPQYVAFVKTV\r\nGHRDNINEEVLRELGLSEEKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKK\r\nLEDYIDRAMDDVAPNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLR\r\nTGAKPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGEYIAEELKKELEA\r\nRIREIKEKYPKPPKRKREERKGKKPWKKDKKKKKKKEKPRRR",
          "organism": "Pyrococcus furiosus",
          "uniprot_code": "Q8U4M1",
          "uniprot_range_first": 1,
          "uniprot_range_last": 402,
          "oligomerization": "dimer",
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          "mw": 46.788,
          "total_mw": 93.576,
          "number_molecules": 2,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "pyrococcus furiosus sR26 stabilized construct",
          "short_name": "st-sR26",
          "sequence": ">st-sR26\r\nGCGAGCAAUGAUGAGUGAUGGGCGAACUGAGCUCGAAAGAGCAAUGAUGACGGAGGUGAUCACUGAGCUCGC",
          "organism": "Pyrococcus furiosus",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "RNA",
          "uniprot_sequence": null,
          "mw": 23.548,
          "total_mw": 23.548,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        },
        {
          "long_name": "Pyrococcus furiosus sR26 substrate D",
          "short_name": "Substrate D",
          "sequence": ">Substrate D\r\nGUAGAUCACCUCCG",
          "organism": "Pyrococcus furiosus",
          "uniprot_code": null,
          "uniprot_range_first": null,
          "uniprot_range_last": null,
          "oligomerization": "monomer",
          "molecular_type": "RNA",
          "uniprot_sequence": null,
          "mw": 4.486,
          "total_mw": 4.486,
          "number_molecules": 1,
          "complex_state": false,
          "deuteration": null,
          "molecule_source": "biological",
          "molecule_description": null
        }
      ],
      "buffer": {
        "name": "50 mM phosphate 500 mM NaCl",
        "concentration_unit": null,
        "comment": null,
        "additive": null,
        "concentration": null,
        "pka": null,
        "ph": 6.6,
        "deuteration": null
      },
      "purity_method": null,
      "name": "Pyrococcus furiosus Box C/D sRNP reconstituted with st-sR6 sRNA bound to substrate D (SAXS data)",
      "ext_coefficient": null,
      "contrast": null,
      "specific_vol": null,
      "dry_vol": null,
      "absorbption": null,
      "deuteration": null,
      "mixture": null
    },
    "contributor": [
      {
        "affiliation": [
          {
            "short_name": null,
            "address": "Germany",
            "full_name": "Leibniz University of Hannover",
            "webpage": "https://www.uni-hannover.de"
          }
        ],
        "contributor_name": "Andrea",
        "contributor_surname": "Graziadei",
        "orcid": "https://orcid.org/0000-0001-7709-6002"
      }
    ],
    "concentration_method": null,
    "concentration_unit": null,
    "date": "2015-07-13",
    "storage_temperature": 20.0,
    "cell_temperature": 40.1,
    "exposure_time": 1.0,
    "number_of_frames": 10,
    "wavelength": 0.09919,
    "sample_detector_distance": 2.864,
    "concentration_min": null,
    "concentration_max": 5.0,
    "sample_volume": null,
    "flow_rate": null,
    "s_min": 0.033,
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    "total_exposure_time": null,
    "seccolumn": null
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  "fits": [],
  "estimated_volume_method": null,
  "pddf_software": "ATSAS GNOM",
  "pddf_software_version": "4.6",
  "i0_calibration_standard": null,
  "description": null,
  "experiment_description": "Synchrotron SAXS data from solutions of Pyrococcus furiosus Box C/D sRNP reconstituted with st-sR6 sRNA bound to substrate D in 50 mM phosphate 500 mM NaCl, pH 6.6 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 5.00 mg/ml was measured at 40.1°C. 10 successive 1 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": "arbitrary",
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  "experimental_mw_error": null,
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  "guinier_i0_error": 0.1,
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  "guinier_rg_error": 0.01,
  "pddf_dmax": 17.0,
  "pddf_dmax_error": null,
  "porod_volume": 429.0,
  "porod_volume_error": null,
  "estimated_volume": null,
  "estimated_volume_error": null,
  "guinier_point_first": 16,
  "guinier_point_last": 49,
  "pddf_point_first": null,
  "pddf_point_last": null,
  "i0_calibration_standard_data": null,
  "intensities_log_log_plot": "SASDGA3_datloglog_img.png",
  "symmetry": null,
  "last_modified": "2020-03-25T10:04:13.882830+01:00",
  "bragg_peak": []
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