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": "SASDBS6",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/A",
"project": {
"title": "Structural and biochemical analysis of <i>Escherichia coli</i> ObgE, a central regulator of bacterial persistence.",
"publication": {
"title": "Structural and biochemical analysis of <i>Escherichia coli</i> ObgE, a central regulator of bacterial persistence.",
"author_list": "Gkekas S, Singh RK, Shkumatov AV, Messens J, Fauvart M, Verstraeten N, Michiels J, Versées W",
"journal": "J Biol Chem",
"doi": "10.1074/jbc.M116.761809",
"pmid": "28223358",
"published_date": "2017 Apr 7"
},
"status": "released",
"submitted_date": "2016-09-28",
"released_date": "2017-02-23"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBS6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBS6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBS6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBS6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBS6.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": "GTPase ObgE/CgtA",
"short_name": "ObgE_FL",
"sequence": "MKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEADENLNTLIDYRFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQGTGETMGDMTKHGQRLLVAKGGWHGLGNTRFKSSVNRTPRQKTNGTPGDKRELLLELMLLADVGMLGMPNAGKSTFIRAVSAAKPKVADYPFTTLVPSLGVVRMDNEKSFVVADIPGLIEGAAEGAGLGIRFLKHLERCRVLLHLIDIDPIDGTDPVENARIIISELELYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAIAEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVAQAEEAKQPEKVEFMWDDYHRQQLEEIAEEDDEDWDDDWDEDDEEGVEFIYKRSAWSHPQFEK",
"organism": "Escherichia coli",
"uniprot_code": "P42641",
"uniprot_range_first": 1,
"uniprot_range_last": 390,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEADENLNTLIDYR\nFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQGTGETMGDMTKHGQRLLVAKG\nGWHGLGNTRFKSSVNRTPRQKTNGTPGDKRELLLELMLLADVGMLGMPNAGKSTFIRAVS\nAAKPKVADYPFTTLVPSLGVVRMDNEKSFVVADIPGLIEGAAEGAGLGIRFLKHLERCRV\nLLHLIDIDPIDGTDPVENARIIISELEKYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAI\nAEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVVQAEEAKQPEKVEFMWDDYHRQQ\nLEEIAEEDDEDWDDDWDEDDEEGVEFIYKR",
"mw": 44.441,
"total_mw": 44.441,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Hepes , 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Apo form of full length ObgE from E.coli (ObgE_FL)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "VUB",
"address": "Pleinlaan 2 1050 Brussel ",
"full_name": "Vrije Universiteit Brussel",
"webpage": "http://www.vub.ac.be/"
}
],
"contributor_name": "Alexander",
"contributor_surname": "Shkumatov",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-06-17",
"storage_temperature": 10.0,
"cell_temperature": 10.0,
"exposure_time": 2.8,
"number_of_frames": 255,
"wavelength": 0.103,
"sample_detector_distance": 1.987,
"concentration_min": 10.0,
"concentration_max": null,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.061,
"s_max": 5.535,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS6_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "r6293",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS6_fit1_model1.pdb",
"model_mw": 46.72,
"bead_radius": 3.5,
"log": "https://www.sasbdb.org/media/log_files/refine_b5VHmZU.log",
"symmetry": "P1",
"comment": "",
"user": 104
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBS6_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 13.1,
"p_value": 0.0001,
"fit_residual_plot": "SASDBS6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBS6_fit1.fir",
"fit_log": null,
"software_version": "",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS6_fit2_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS6_fit2_model1.pdb",
"model_mw": 44.4,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "",
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS6_fit2_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS6_fit2_model2.pdb",
"model_mw": 44.4,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "",
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS6_fit2_model3_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS6_fit2_model3.pdb",
"model_mw": 44.4,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "",
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS6_fit2_model4_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS6_fit2_model4.pdb",
"model_mw": 44.4,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "",
"user": 104
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBS6_fit2_model5_img.png",
"software": "EOM/RANCH",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDBS6_fit2_model5.pdb",
"model_mw": 44.4,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "",
"user": 104
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBS6_fit2_fixed_fit_img.png",
"software": null,
"chi_square_value": 11.4,
"p_value": 0.0001,
"fit_residual_plot": "fit4columns510_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBS6_fit2.fit",
"fit_log": null,
"software_version": "",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM 5.0 (r4547)",
"i0_calibration_standard": null,
"description": "SAXS-based ensemble modelling of ObgE_FL taking into account the flexibility of the C-terminal\r\ndomain.\r\nThe sample protein includes a C-terminal Strep-tag; frames corresponding to the peak in HPLC-SAXS run were averaged using DATAVER v0.2 (r3709)",
"experiment_description": "Synchrotron SAXS data from solutions of the Apo form of full length ObgE from E.coli (ObgE_FL) in 20 mM HEPES , 300 mM NaCl, 250 mM imidazole, 5 mM MgCl2, 2 mM DTT, pH 7.5, were collected at the SWING beam line at the SOLEIL Synchrotron (Saint-Aubin, France) using a CCD AVIEX detector at a sample-detector distance of 2.0 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Data collection was performed at at 10°C. 255 successive 2.8 second frames were collected through an HPLC-SEC elution peak. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the different curves were scaled for protein concentration, then averaged to produce the final SAXS profile displayed in this entry.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 55.4,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 60.0,
"porod_mw_error": null,
"pddf_i0": 0.03904,
"pddf_i0_error": 0.0003,
"guinier_i0": 0.0383,
"guinier_i0_error": 2.7e-05,
"pddf_rg": 3.96,
"pddf_rg_error": 0.1,
"guinier_rg": 3.7,
"guinier_rg_error": 0.1,
"pddf_dmax": 18.1,
"pddf_dmax_error": null,
"porod_volume": 102.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 18,
"guinier_point_last": 46,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDBS6_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:28:07.504745+02:00",
"bragg_peak": []
}
