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": "SASDCQ7",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/A",
"project": {
"title": "Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors.",
"publication": {
"title": "Structural Dynamics Control Allosteric Activation of Cytohesin Family Arf GTPase Exchange Factors.",
"author_list": "Malaby AW, Das S, Chakravarthy S, Irving TC, Bilsel O, Lambright DG",
"journal": "Structure",
"doi": "10.1016/j.str.2017.11.019",
"pmid": "29276036",
"published_date": "2018 Jan 2"
},
"status": "released",
"submitted_date": "2017-09-22",
"released_date": "2018-01-02"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCQ7.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCQ7.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCQ7_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCQ7_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCQ7_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCQ7_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCQ7.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "MAR 165 CCD",
"resolution": null
},
"name": "Advanced Photon Source (APS), Argonne National Laboratory",
"city": "Lemont, IL",
"country": "USA",
"beamline_name": "BioCAT 18ID",
"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": "Grp1 63-399 E161A Arf6 Q67L fusion protein",
"short_name": null,
"sequence": "MGHHHHHHGSTTQRNAQIAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYLGER\r\nDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCNPGVFQSTDTCYVL\r\nSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLYESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSH\r\nKGQVIKACKTEADGRVVEGNHVVYRISAPSPEEKEEWMKSIKASISRDPFYDMLATRKRRIANKKGKVLSKIFGNKEMRILM\r\nLGLDAAGKTTILYKLKLGQSVTTIPTVGFNVETVTYKNVKFNVWDVGGLDKIRPLWRHYYTGTQGLIFVV\r\nDCADRDRIDEARQELHRIINDREMRDAIILIFANKQDLPDAMKPHEIQEKLGLTRIRDRNWYVQPSCATS\r\nGDGLYEGLTWLTSNYN",
"organism": "Mus musculus",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 60.146,
"total_mw": 60.146,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM Tris, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, 5% glycerol, 0.001 mM insitol 1,3,4,5-tetrakis phosphate",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 8.0,
"deuteration": null
},
"purity_method": null,
"name": "Truncated monomeric Cytohesin-3 (Grp1; amino acids 63-399) E161A Arf6 Q67L fusion protein",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "UMASS",
"address": "Worcester, MA, USA",
"full_name": "UMASS Medical School",
"webpage": "https://www.umassmed.edu/"
}
],
"contributor_name": "David",
"contributor_surname": "Lambright",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2013-11-15",
"storage_temperature": null,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 1,
"wavelength": 0.10332,
"sample_detector_distance": 2.5,
"concentration_min": 0.0,
"concentration_max": 2.3,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.069,
"s_max": 3.162,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCQ7_fit1_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "CORAL05",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCQ7_fit1_model1.pdb",
"model_mw": 61.08,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/coral_ooYOuNj.log",
"symmetry": "P1",
"comment": "Sec7 domain derived from 2R09; MSE converted to MET; PH domain and Arf6 derived from 2KAX",
"user": 241
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCQ7_fit1_fixed_fit_img.png",
"software": "CORAL",
"chi_square_value": 1.53,
"p_value": 0.00046,
"fit_residual_plot": "SASDCQ7_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCQ7_fit1.fit",
"fit_log": null,
"software_version": "CORAL05",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCQ7_fit2_model1_img.png",
"software": "EOM/RANCH",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "2.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCQ7_fit2_model1.pdb",
"model_mw": 61.08,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/Rancheom_BrOQm0o.log",
"symmetry": "P1",
"comment": "Sec7 domain derived from 2R09; MSE converted to MET; PH domain and Arf6 derived from 2KAX",
"user": 241
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCQ7_fit2_model2_img.png",
"software": "EOM/RANCH",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "2.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCQ7_fit2_model2.pdb",
"model_mw": 61.08,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/Rancheom_TFEn5AX.log",
"symmetry": "P1",
"comment": "Sec7 domain derived from 2R09; MSE converted to MET; PH domain and Arf6 derived from 2KAX",
"user": 241
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCQ7_fit2_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 1.67,
"p_value": 0.0039,
"fit_residual_plot": "fit4columns1108_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCQ7_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/gajoe_noUK8iJ.log",
"software_version": "2.0",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCQ7_fit3_model1_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "MultiFoXS",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCQ7_fit3_model1.pdb",
"model_mw": 61.17,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "Sec7 domain derived from 2R09; MSE converted to MET; PH domain and Arf6 derived from 2KAX",
"user": 241
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCQ7_fit3_model2_img.png",
"software": "Other",
"pdb_link": [
{
"pdb_code": "2r09",
"ext_code": "2R09",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "MultiFoXS",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCQ7_fit3_model2.pdb",
"model_mw": 61.17,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "Sec7 domain derived from 2R09; MSE converted to MET; PH domain and Arf6 derived from 2KAX",
"user": 241
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCQ7_fit3_fitfoxs_img.png",
"software": "Other",
"chi_square_value": 1.62,
"p_value": 0.000465,
"fit_residual_plot": "SASDCQ7_fit3_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCQ7_fit3.dat",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/multifoxs_ensembles_size_G0vqVKs.txt",
"software_version": "MultiFoXS",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "5.0",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "This experimental profile was derived from SEC-SAXS data collected at the BioCAT Sector 18-ID beamline at the Argonne National Laboratory Advanced Photon Source using a MAR 165 CCD detector. The protein was equilibrated with a 1.2 molar excess of inositol 1,3,4,5-tetrakis phosphate (IP4), concentrated to 10 mg/ml, and injected in 0.1 ml onto a 3 ml Superdex-200 Increase column equilibrated with 20 mM Tris, pH 8.0, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, 5% glycerol, and 0.001 ml IP4. SAXS data sets were acquired with 1 s exposures at 5 s intervals during elution at a flow rate of 0.25 ml/min. Raw SAXS images were radially averaged on a log scale over the q range 0.00621-0.333 Å-1 and normalized by the incident beam intensity. The protein scattering profile was reconstructed by singular value decomposition and linear combination (SVD-LC) as described in Malaby et al. (2015) Methods for analysis of size-exclusion chromatography-small angle X-ray scattering and reconstruction of protein scattering. J Appl Crystallogr 48: 1102-1113.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 57.5,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 57.5,
"porod_mw_error": null,
"pddf_i0": 1.01,
"pddf_i0_error": 0.001,
"guinier_i0": 1.01,
"guinier_i0_error": 0.0008,
"pddf_rg": 3.13,
"pddf_rg_error": 0.007,
"guinier_rg": 3.14,
"guinier_rg_error": 0.01,
"pddf_dmax": 11.6,
"pddf_dmax_error": 0.1,
"porod_volume": 86.2,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 31,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCQ7_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-08-28T15:28:09.410742+02:00",
"bragg_peak": []
}
