The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
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{
"code": "SASDEZ3",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "Inhibitor-induced dimerization of an essential oxidoreductase from African Trypanosomes.",
"publication": {
"title": "Inhibitor-induced dimerization of an essential oxidoreductase from African Trypanosomes.",
"author_list": "Wagner A, Le TA, Brennich M, Klein P, Bader N, Diehl E, Paszek D, Weickhmann AK, Dirdjaja N, Krauth-Siegel RL, Engels B, Opatz T, Schindelin H, Hellmich UA",
"journal": "Angew Chem Int Ed Engl",
"doi": "10.1002/anie.201810470",
"pmid": "30605929",
"published_date": "2019 Jan 3"
},
"status": "released",
"submitted_date": "2018-09-06",
"released_date": "2019-01-08"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEZ3.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEZ3.dat",
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"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEZ3_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEZ3_pofr_img.png",
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"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEZ3.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": "Tryparedoxin",
"short_name": null,
"sequence": "GSGLAKYLPGATNLLSKSGEVSLGSLVGKTVFLYFSASWCPPCRG\r\nFTPVLAEFYEKHHVAKNFEVVLISWDENESDFHDYYGKMPWLALPFDQRSTVSELGKTFG\r\nVESIPTLITINADTGAIIGTQARTRVIEDPDGANFPWPN",
"organism": "Trypanosoma brucei brucei",
"uniprot_code": "O77404",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MSGLAKYLPGATNLLSKSGEVSLGSLVGKTVFLYFSASWCPPCRGFTPVLAEFYEKHHVA\nKNFEVVLISWDENESDFHDYYGKMPWLALPFDQRSTVSELGKTFGVESIPTLITINADTG\nAIIGTQARTRVIEDPDGANFPWPN",
"mw": 15.817,
"total_mw": 15.817,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "10 mM HEPES pH 7.5, 50 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Tryparedoxin, oxidized state",
"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": "2018-05-31",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": null,
"wavelength": 0.099,
"sample_detector_distance": 2.869,
"concentration_min": null,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.037,
"s_max": 4.928,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ3_fit1_model1_img.png",
"software": "GASBOR",
"pdb_link": [],
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"type_of_model": "dummy",
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"model_mw": null,
"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/gasP1_2_fit_img.png",
"software": "GASBOR",
"chi_square_value": 1.79,
"p_value": 0.000382,
"fit_residual_plot": "gasP1_2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ3_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/gasP1_2.log",
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ3_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ3_fit2_model1.pdb",
"model_mw": 15.77,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/run2.log",
"symmetry": null,
"comment": null,
"user": 119
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/run2-1_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.63,
"p_value": 0.001909,
"fit_residual_plot": "run2-1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ3_fit2.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ3_fit3_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6gxy",
"ext_code": "6GXY",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ3_fit3_model1.pdb",
"model_mw": 15.88,
"bead_radius": null,
"log": null,
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"comment": null,
"user": 119
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEZ3_fit3_model2_img.png",
"software": "Other",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEZ3_fit3_model2.pdb",
"model_mw": 31.77,
"bead_radius": null,
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}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/TpxWTox_1030_1049_crp_B8czgTu_fit_img.png",
"software": "OLIGOMER",
"chi_square_value": 2.4,
"p_value": 0.0,
"fit_residual_plot": "TpxWTox_1030_1049_crp_B8czgTu_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEZ3_fit3.fit",
"fit_log": null,
"software_version": null,
"description": "Fit to mixture of crystallographic monomer and dimer: 99.9% monomer"
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": "SEC column type: GE Healthcare S75 3.2/300; Sample Injection Concentration = 10 mg/mL;\r\nColumn flow-rate = 0.1 mL/min.",
"experiment_description": "Synchrotron SAXS data from solutions of Tryparedoxin, oxidized state, in 10 mM HEPES pH 7.5, 50 mM NaCl, pH 7.5 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data were collected using in-line size exclusion chromatography (SEC)-SAXS at 20°C.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 16.1,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 16.1,
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"pddf_i0": 10.69,
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"guinier_i0": 10.69,
"guinier_i0_error": 0.01,
"pddf_rg": 1.621,
"pddf_rg_error": null,
"guinier_rg": 1.61,
"guinier_rg_error": 0.12,
"pddf_dmax": 6.5,
"pddf_dmax_error": null,
"porod_volume": 27.46,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 24,
"guinier_point_last": 162,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEZ3_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
