The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDFL8",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Defects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.",
"publication": {
"title": "Defects in t<sup>6</sup>A tRNA modification due to GON7 and YRDC mutations lead to Galloway-Mowat syndrome.",
"author_list": "Arrondel C, Missoury S, Snoek R, Patat J, Menara G, Collinet B, Liger D, Durand D, Gribouval O, Boyer O, Buscara L, Martin G, Machuca E, Nevo F, Lescop E, Braun DA, Boschat AC, Sanquer S, Guerrera IC, Revy P, Parisot M, Masson C, Boddaert N, Charbit M, Decramer S, Novo R, Macher MA, Ranchin B, Bacchetta J, Laurent A, Collardeau-Frachon S, van Eerde AM, Hildebrandt F, Magen D, Antignac C, van Tilbeurgh H, Mollet G",
"journal": "Nat Commun",
"doi": "10.1038/s41467-019-11951-x",
"pmid": "31481669",
"published_date": "2019 Sep 3"
},
"status": "released",
"submitted_date": "2019-07-05",
"released_date": "2019-09-05"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDFL8.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDFL8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFL8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFL8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDFL8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDFL8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDFL8.sascif",
"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,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "EKC/KEOPS complex subunit GON7",
"short_name": "GON7",
"sequence": "MELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTEL\r\nFDPLVQGEVQHRVAAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPSHHHHHH",
"organism": "Homo sapiens",
"uniprot_code": "Q9BXV9",
"uniprot_range_first": 1,
"uniprot_range_last": 100,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MELLGEYVGQEGKPQKLRVSCEAPGDGDPFQGLLSGVAQMKDMVTELFDPLVQGEVQHRV\nAAAPDEDLDGDDEDDAEDENNIDNRTNFDGPSAKRPKTPS",
"mw": 11.682,
"total_mw": 11.682,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "EKC/KEOPS complex subunit LAGE3",
"short_name": "LAGE3",
"sequence": "MRDADADAGGGADGGDGRGGHSCRGGV\r\nDTAAAPAGGAPPAHAPGPGRDAASAARGSRMRPHIFTLSVPFPTPLEAEIAHGSLAPDAE\r\nPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISVINFLDQLSLVVRTMQRFGPPVSR",
"organism": "Homo sapiens",
"uniprot_code": "Q14657",
"uniprot_range_first": 1,
"uniprot_range_last": 143,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MRDADADAGGGADGGDGRGGHSCRGGVDTAAAPAGGAPPAHAPGPGRDAASAARGSRMRP\nHIFTLSVPFPTPLEAEIAHGSLAPDAEPHQRVVGKDLTVSGRILVVRWKAEDCRLLRISV\nINFLDQLSLVVRTMQRFGPPVSR",
"mw": 14.804,
"total_mw": 14.804,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Probable tRNA N6-adenosine threonylcarbamoyltransferase",
"short_name": "OSGEP",
"sequence": "MPAVLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGDTARHHRAVILDLLQE\r\nALTESGLTSQDIDCIAYTKGPGMGAPLVSVAVVARTVAQLWNKPLVGVNHCIGHIEMGRL\r\nITGATSPTVLYVSGGNTQVIAYSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYN\r\nIEQMAKRGKKLVELPYTVKGMDVSFSGILSFIEDVAHRMLATGECTPEDLCFSLQETVFA\r\nMLVEITERAMAHCGSQEALIVGGVGCNVRLQEMMATMCQERGARLFATDERFCIDNGAMIAQAGWEMFRAGHRTPLSDSGVTQRYRTDEVEVTWRD",
"organism": "Homo sapiens",
"uniprot_code": "Q9NPF4",
"uniprot_range_first": 1,
"uniprot_range_last": 335,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MPAVLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGDTARHHRAVILDLLQEA\nLTESGLTSQDIDCIAYTKGPGMGAPLVSVAVVARTVAQLWNKPLVGVNHCIGHIEMGRLI\nTGATSPTVLYVSGGNTQVIAYSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNI\nEQMAKRGKKLVELPYTVKGMDVSFSGILSFIEDVAHRMLATGECTPEDLCFSLQETVFAM\nLVEITERAMAHCGSQEALIVGGVGCNVRLQEMMATMCQERGARLFATDERFCIDNGAMIA\nQAGWEMFRAGHRTPLSDSGVTQRYRTDEVEVTWRD",
"mw": 36.426,
"total_mw": 36.426,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 6.5,
"deuteration": null
},
"purity_method": null,
"name": "GON7, the fifth subunit of human KEOPS, bound to LAGE3-OSGEP (EKC/KEOPS complex subunit:Probable tRNA N6-adenosine threonylcarbamoyltransferase)",
"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": "sophia",
"contributor_surname": "missoury",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-05-12",
"storage_temperature": null,
"cell_temperature": 15.0,
"exposure_time": 1.0,
"number_of_frames": 255,
"wavelength": 0.1,
"sample_detector_distance": 1.8,
"concentration_min": null,
"concentration_max": 1.48,
"sample_volume": 65.0,
"flow_rate": 0.3,
"s_min": 0.101,
"s_max": 5.003,
"total_exposure_time": null,
"seccolumn": 10
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDFL8_fit1_model1_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "6gwj",
"ext_code": "6GWJ",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDFL8_fit1_model1.pdb",
"model_mw": 62.51,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 299
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/BunchModelGON7-LAGE3-OSGEP00_LmrrGpl_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.308,
"p_value": 0.001285,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDFL8_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/BunchModelGON7-LAGE3-OSGEP00_rg0eWvM.log",
"software_version": "2.8.3",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. SAXS data were normalized to the intensity of the incident beam, averaged and background subtracted using the program US-SOMO. Frames were examined individually and 21 identical frames were averaged and further processed. The corresponding SEC-elution concentration was approximately 0.35 mg/mL.\r\nThe complex is constituted of one monomer of OSGEP, one monomer of LAGE3 and one monomer of GON7. Molecular mass was obtained using the Bayesian inference approach proposed in PRIMUS/qt, which combines four concentration independent MM estimators: M=59.5 kDa within the credibility interval [57.5-64.5].",
"experiment_description": "Synchrotron SAXS data from solutions of GON7 bound to LAGE3-OSGEP in 20 mM MES, 200 mM NaCl, 5 mM β-mercaptoethanol, pH 6.5 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a AVIEX PCCD170170 detector at a sample-detector distance of 1.8 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 65.00 μl sample at 1.5 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 15°C. 255 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": "1/cm",
"experimental_mw": 59.5,
"experimental_mw_error": null,
"guinier_i0_mw": 58.5,
"guinier_i0_mw_error": null,
"porod_mw": 57.0,
"porod_mw_error": null,
"pddf_i0": 0.01634,
"pddf_i0_error": null,
"guinier_i0": 0.01625,
"guinier_i0_error": 2e-05,
"pddf_rg": 3.14,
"pddf_rg_error": null,
"guinier_rg": 3.06,
"guinier_rg_error": 0.06,
"pddf_dmax": 11.5,
"pddf_dmax_error": null,
"porod_volume": 91.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 58,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDFL8_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-07-03T15:31:49.852616+02:00",
"bragg_peak": []
}
