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": "SASDEP9",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/nm",
"project": {
"title": "cGAS facilitates sensing of extracellular cyclic dinucleotides to activate innate immunity.",
"publication": {
"title": "cGAS facilitates sensing of extracellular cyclic dinucleotides to activate innate immunity.",
"author_list": "Liu H, Moura-Alves P, Pei G, Mollenkopf HJ, Hurwitz R, Wu X, Wang F, Liu S, Ma M, Fei Y, Zhu C, Koehler AB, Oberbeck-Mueller D, Hahnke K, Klemm M, Guhlich-Bornhof U, Ge B, Tuukkanen A, Kolbe M, Dorhoi A, Kaufmann SH",
"journal": "EMBO Rep",
"doi": "10.15252/embr.201846293",
"pmid": "30872316",
"published_date": "2019 Mar 14"
},
"status": "released",
"submitted_date": "2019-01-14",
"released_date": "2019-03-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEP9.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEP9.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP9_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP9_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEP9_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEP9_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEP9.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": "Cyclic GMP-AMP synthase",
"short_name": "cGAS",
"sequence": "MQPWHGKAMQRASEAGATAPKASARNARGAPMDPTESPAAPEAALPKAGKFGPARKSGSRQKKSAPDTQERPPVRATGARAKKAPQRAQDTQPSDATSAPGAEGLEPPAAREPALSRAGSCRQRGARCSTKPRPPPGPWDVPSPGLPVSAPILVRRDAAPGASKLRAVLEKLKLSRDDISTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLEEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKRKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLVPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQLKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKLENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEFLEYPYDVPDYAAAALEHHHHHH",
"organism": "Homo sapiens",
"uniprot_code": "Q8N884",
"uniprot_range_first": 1,
"uniprot_range_last": 522,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MQPWHGKAMQRASEAGATAPKASARNARGAPMDPTESPAAPEAALPKAGKFGPARKSGSR\nQKKSAPDTQERPPVRATGARAKKAPQRAQDTQPSDATSAPGAEGLEPPAAREPALSRAGS\nCRQRGARCSTKPRPPPGPWDVPSPGLPVSAPILVRRDAAPGASKLRAVLEKLKLSRDDIS\nTAAGMVKGVVDHLLLRLKCDSAFRGVGLLNTGSYYEHVKISAPNEFDVMFKLEVPRIQLE\nEYSNTRAYYFVKFKRNPKENPLSQFLEGEILSASKMLSKFRKIIKEEINDIKDTDVIMKR\nKRGGSPAVTLLISEKISVDITLALESKSSWPASTQEGLRIQNWLSAKVRKQLRLKPFYLV\nPKHAKEGNGFQEETWRLSFSHIEKEILNNHGKSKTCCENKEEKCCRKDCLKLMKYLLEQL\nKERFKDKKHLDKFSSYHVKTAFFHVCTQNPQDSQWDRKDLGLCFDNCVTYFLQCLRTEKL\nENYFIPEFNLFSSNLIDKRSKEFLTKQIEYERNNEFPVFDEF",
"mw": 61.419,
"total_mw": 61.419,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Cyclic GMP-AMP synthase (cGAS)",
"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": "Anne",
"contributor_surname": "Tuukkanen",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-04-25",
"storage_temperature": 10.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 3600,
"wavelength": 0.124,
"sample_detector_distance": 3.0,
"concentration_min": null,
"concentration_max": 9.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.185,
"s_max": 5.025,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP9_fit1_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEP9_fit1_model1.pdb",
"model_mw": 62.53,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 27
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP9_fit1_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEP9_fit1_model2.pdb",
"model_mw": 62.53,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 27
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP9_fit1_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEP9_fit1_model3.pdb",
"model_mw": 62.53,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 27
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP9_fit1_model4_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEP9_fit1_model4.pdb",
"model_mw": 62.53,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 27
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP9_fit1_model5_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEP9_fit1_model5.pdb",
"model_mw": 62.53,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 27
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEP9_fit1_model6_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "mix",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEP9_fit1_model6.pdb",
"model_mw": 62.53,
"bead_radius": 1.9,
"log": null,
"symmetry": null,
"comment": null,
"user": 27
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEP9_fit1_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.211,
"p_value": 0.006468,
"fit_residual_plot": "SASDEP9_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEP9_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of cyclic GMP-AMP synthase (cGAS) in 20 mM HEPES, pH 7.4 were measured using size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at the PETRA III storage ring (Hamburg, Germany) using a Pilatus 2M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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: XXXX ; Flow rate: 0.5 mL/min; Total acquisition time: 3600 x 1 s frames; Sample injection concentration: 9 mg/mL; Injection volume: 75 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": 64.7,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 64.7,
"porod_mw_error": null,
"pddf_i0": 2237.0,
"pddf_i0_error": 22.4,
"guinier_i0": 2166.9,
"guinier_i0_error": 18.2,
"pddf_rg": 3.384,
"pddf_rg_error": 0.2,
"guinier_rg": 3.14,
"guinier_rg_error": 1.4,
"pddf_dmax": 12.69,
"pddf_dmax_error": 0.6,
"porod_volume": 110.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 14,
"guinier_point_last": 84,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEP9_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-06-21T07:56:39.492710+02:00",
"bragg_peak": []
}
