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.
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{
"code": "SASDED7",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain.",
"publication": {
"title": "Structure of the Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain.",
"author_list": "Viet KK, Wagner A, Schwickert K, Hellwig N, Brennich M, Bader N, Schirmeister T, Morgner N, Schindelin H, Hellmich UA",
"journal": "Structure",
"doi": "10.1016/j.str.2019.04.016",
"pmid": "31178222",
"published_date": "2019 May 14"
},
"status": "released",
"submitted_date": "2018-10-30",
"released_date": "2019-06-11"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDED7.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDED7.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDED7_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDED7_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDED7_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDED7_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDED7.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": {
"molecule": [
{
"long_name": "Transient receptor potential channel mucolipin 2",
"short_name": "TRPML2",
"sequence": "GLSNQLVVAFKEDNTVAFKHLFLKGYSGTDEDDYSCS\r\nVYTQEDAYESIFFAINQYHQLKDITLGTLGYGENEDNRIGLKVCKQHYKKGTMFPSNETL\r\nNIDNDVELDCVQLDLQDLSKKPPDWKNSSFFRLEFYRLLQVEISFHLKGIDLQTIHSREL\r\nPDCYVFQNTIIFDNKAHSGKIKIYFDSDAKIEECKDLNIFGSTQK",
"organism": "Homo sapiens",
"uniprot_code": "Q8IZK6",
"uniprot_range_first": 1,
"uniprot_range_last": 285,
"oligomerization": "tetramer",
"molecular_type": "protein",
"uniprot_sequence": "MARQPYRFPQARIPERGSGVFRLTVRNAMAHRDSEMKEECLREDLKFYFMSPCEKYRARR\nQIPWKLGLQILKIVMVTTQLVRFGLSNQLVVAFKEDNTVAFKHLFLKGYSGTDEDDYSCS\nVYTQEDAYESIFFAINQYHQLKDITLGTLGYGENEDNRIGLKVCKQHYKKGTMFPSNETL\nNIDNDVELDCVQLDLQDLSKKPPDWKNSSFFRLEFYRLLQVEISFHLKGIDLQTIHSREL\nPDCYVFQNTIIFDNKAHSGKIKIYFDSDAKIEECKDLNIFGSTQKNAQYVLVFDAFVIVI\nCLASLILCTRSIVLALRLRKRFLNFFLEKYKRPVCDTDQWEFINGWYVLVIISDLMTIIG\nSILKMEIKAKNLTNYDLCSIFLGTSTLLVWVGVIRYLGYFQAYNVLILTMQASLPKVLRF\nCACAGMIYLGYTFCGWIVLGPYHDKFENLNTVAECLFSLVNGDDMFATFAQIQQKSILVW\nLFSRLYLYSFISLFIYMILSLFIALITDSYDTIKKFQQNGFPETDLQEFLKECSSKEEYQ\nKESSAFLSCICCRRRKRSDDHLIPIS",
"mw": 23.354,
"total_mw": 93.416,
"number_molecules": 4,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM HEPES pH 7.4, 150 mM NaCl, 2 mM CaCl2",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain at pH 7.4, 2mM Calcium",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "EMBL",
"address": "Grenoble, France",
"full_name": "European Molecular Biology Laboratory (EMBL) - Grenoble Outstation",
"webpage": "https://www.embl.fr/"
}
],
"contributor_name": "Martha",
"contributor_surname": "Brennich",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-10-20",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 1200,
"wavelength": 0.099,
"sample_detector_distance": 2.849,
"concentration_min": 0.0,
"concentration_max": 0.55,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.035,
"s_max": 4.946,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDED7_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDED7_fit1_model1.pdb",
"model_mw": 92.32,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/pH7520CaCRP_P1start295_20-1_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.08,
"p_value": 0.003595,
"fit_residual_plot": "pH7520CaCRP_P1start295_20-1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDED7_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pH7520CaCRP_P1start295_20.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDED7_fit2_model1_img.png",
"software": "DAMMIF",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r10552",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDED7_fit2_model1.pdb",
"model_mw": 92.8,
"bead_radius": 1.8,
"log": null,
"symmetry": null,
"comment": null,
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/pH7520Ca89_P1_OBLATE_02_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 1.106,
"p_value": 0.607589,
"fit_residual_plot": "pH7520Ca89_P1_OBLATE_02_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDED7_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/pH7520Ca89_P1_OBLATE_02.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "The experimental mass was determined via correlated volume.",
"experiment_description": "Synchrotron SAXS data from solutions of Human TRPML2 Ion Channel Extracytosolic/Lumenal Domain in 10 mM HEPES pH 7.4, 150 mM NaCl, 2 mM CaCl2, were collected using size exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20°C using the following parameters: Column: Agilent BioSEC 3 bead size 300 μm, Ø 4.6 mm, length 300 mm; Flow rate: 0.3 mL/min; Total acquisition time: 20 min; Injection concentration: 10 mg/mL; Injection volume: 20 μL. The data obtained through the sample elution peak were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 96.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 84.0,
"porod_mw_error": null,
"pddf_i0": 46.25,
"pddf_i0_error": null,
"guinier_i0": 46.48,
"guinier_i0_error": 0.12,
"pddf_rg": 3.362,
"pddf_rg_error": null,
"guinier_rg": 3.39,
"guinier_rg_error": 0.4,
"pddf_dmax": 8.9,
"pddf_dmax_error": null,
"porod_volume": 134.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 13,
"guinier_point_last": 74,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDED7_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
