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": "SASDEG8",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Farnesylation of human guanylate binding protein 1 as safety mechanism preventing structural rearrangements and uninduced dimerization.",
"publication": {
"title": "Farnesylation of human guanylate binding protein 1 as safety mechanism preventing structural rearrangements and uninduced dimerization.",
"author_list": "Lorenz C, Ince S, Zhang T, Cousin A, Batra-Safferling R, Nagel-Steger L, Herrmann C, Stadler AM",
"journal": "FEBS J",
"doi": "10.1111/febs.15015",
"pmid": "31330084",
"published_date": "2019 Jul 22"
},
"status": "released",
"submitted_date": "2018-11-27",
"released_date": "2019-07-24"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEG8.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEG8.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEG8_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEG8_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEG8_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEG8_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEG8.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": "human Guanylate-binding protein 1",
"short_name": "hGBP1",
"sequence": ">hGBP1-mitHIStag:A|CHAIN|SEQUENCE\r\nMRGSHHHHHHGSASEIHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDRPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPCMENAVLALAQIENSAAVQKAIAHYEQQMGQKVQLPTESLQELLDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSGLLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQTLTEKEKEIEVERVKAESAQASAKMLQEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRKACTIS",
"organism": "Homo sapiens",
"uniprot_code": "P32455",
"uniprot_range_first": 1,
"uniprot_range_last": 592,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MASEIHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAG\nKKKGFSLGSTVQSHTKGIWMWCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAV\nLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDENENEVEDSADFVSFFPDFVW\nTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDR\nPVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTY\nVNAISSGDLPCMENAVLALAQIENSAAVQKAIAHYEQQMGQKVQLPTETLQELLDLHRDS\nEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQEASSDRCSALLQVIFSPLEE\nEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQ\nTLTEKEKEIEVERVKAESAQASAKMLQEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRV\nQLLKEQERTLALKLQEQEQLLKEGFQKESRIMKNEIQDLQTKMRRRKACTIS",
"mw": 69.169,
"total_mw": 138.338,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM Tris-HCl, 5 mM MgCl2, 150 mM NaCl, 0.2 mM GppNHp",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.9,
"deuteration": null
},
"purity_method": null,
"name": "Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), dimer from SEC-SAXS",
"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": "Forschungszentrum Jülich",
"webpage": "https://www.fz-juelich.de"
}
],
"contributor_name": "Charlotte",
"contributor_surname": "Lorenz",
"orcid": "https://orcid.org/0000-0003-3614-341X"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-04-30",
"storage_temperature": 20.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 3600,
"wavelength": 0.09919,
"sample_detector_distance": 2.867,
"concentration_min": null,
"concentration_max": 55.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.047,
"s_max": 4.944,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEG8_fit1_model1_img.png",
"software": "PyMOL",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEG8_fit1_model1.pdb",
"model_mw": 127.8,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 354
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEG8_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1058.2468,
"p_value": 0.0,
"fit_residual_plot": "SASDEG8_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEG8_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/1F5N-1_1F5N-Dimer00_XOd2Vkk.log",
"software_version": null,
"description": null
},
{
"models": [],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEG8_fit2_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.493,
"p_value": 4.5e-05,
"fit_residual_plot": "SASDEG8_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEG8_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_GppNHp_aHex7Jh.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEG8_fit3_model1_img.png",
"software": "PyMOL",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDEG8_fit3_model1.pdb",
"model_mw": 124.1,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 354
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEG8_fit3_fixed_fit_img.png",
"software": "SASREF",
"chi_square_value": 6.45,
"p_value": 0.0,
"fit_residual_plot": "SASDEG8_fit3_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEG8_fit3.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/09_dimer_7subsP1_run06.log",
"software_version": null,
"description": null
}
],
"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 Human Guanylate Binding Protein 1 with guanylyl imidodiphosphate (hGBP1 + GppNHp) in 50 mM Tris-HCl, 5 mM MgCl2, 150 mM NaCl, 0.2 mM GppNHp pH 7.9 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 2.9 m and at a wavelength of λ = 0.09919 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: UNKNOWN; Flow rate: UNKNOWN mL/min; Total acquisition time: 3600 s; Sample injection concentration: 55 mg/mL; Injection volume: UNKNOWN μL. The data obtained through the sample elution peak (collected as successive 1 s frames) 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": 159.38,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 168.49,
"porod_mw_error": null,
"pddf_i0": 157.4,
"pddf_i0_error": null,
"guinier_i0": 155.5,
"guinier_i0_error": 0.16,
"pddf_rg": 5.728,
"pddf_rg_error": null,
"guinier_rg": 5.45,
"guinier_rg_error": 0.19,
"pddf_dmax": 22.0,
"pddf_dmax_error": null,
"porod_volume": 269.6,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 18,
"guinier_point_last": 32,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDEG8_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:28:11.819155+02:00",
"bragg_peak": []
}
