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": "SASDD89",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.",
"publication": {
"title": "The 3-D structure of VNG0258H/RosR - A haloarchaeal DNA-binding protein in its ionic shell.",
"author_list": "Kutnowski N, Shmuely H, Dahan I, Shmulevich F, Davidov G, Shahar A, Eichler J, Zarivach R, Shaanan B",
"journal": "J Struct Biol",
"doi": "10.1016/j.jsb.2018.08.008",
"pmid": "30110657",
"published_date": "2018 Aug 12"
},
"status": "released",
"submitted_date": "2018-06-29",
"released_date": "2018-08-15"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD89.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD89.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD89_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD89_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD89_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD89_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD89.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": "VNG0258H/RosR",
"short_name": "VNG0258H/RosR",
"sequence": ">VNG0258H/RosR\r\nMSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDL\r\nVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADDAAAL\r\nEHHHHHH",
"organism": "Halobacterium salinarum NRC-1",
"uniprot_code": "Q9HSF4",
"uniprot_range_first": 1,
"uniprot_range_last": 116,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSEAQPDARSDARDLTAFQKNILTVLGEEARYGLAIKRELEEYYGEEVNHGRLYPNLDDL\nVNKGLVEKSELDKRTNEYALTNEGFDAVVDDLEWTLSKFVADADRRERVETIVADD",
"mw": 14.533,
"total_mw": 29.066,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "50 mM HEPES, 2 M KCl, 0.02% NaN3",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.0,
"deuteration": null
},
"purity_method": null,
"name": "Structure of Halobacterium salinarum VNG0258H/RosR in the presence of 2 M KCl",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Israel",
"full_name": "Ben-Gurion University of the Negev",
"webpage": "https://in.bgu.ac.il/"
}
],
"contributor_name": "Nitzan",
"contributor_surname": "kutnowski",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2015-03-07",
"storage_temperature": 25.0,
"cell_temperature": 25.0,
"exposure_time": 2.0,
"number_of_frames": 10,
"wavelength": 0.09919,
"sample_detector_distance": 2.864,
"concentration_min": null,
"concentration_max": 10.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.034,
"s_max": 4.975,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD89_fit1_model1_img.png",
"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD89_fit1_model1.pdb",
"model_mw": 27.295,
"bead_radius": 2.7,
"log": null,
"symmetry": null,
"comment": null,
"user": 339
},
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/2M_KCL_SASDD89_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "5",
"model_data": "https://www.sasbdb.org/media/pdb_file/2M_KCL_SASDD89.pdb",
"model_mw": 33.727,
"bead_radius": 2.75,
"log": null,
"symmetry": null,
"comment": null,
"user": 339
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD89_fit1_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 1.036324,
"p_value": 0.442257,
"fit_residual_plot": "SASDD89_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD89_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/2M_KCl.log",
"software_version": "2.8",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD89_fit2_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "6fdh",
"ext_code": "6FDH",
"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/SASDD89_fit2_model1.pdb",
"model_mw": 25.76,
"bead_radius": null,
"log": "https://www.sasbdb.org/media/log_files/KCl.log",
"symmetry": null,
"comment": null,
"user": 339
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD89_fit2_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 7.656289,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD89_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/KCl.log",
"software_version": "2.8",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "4.6",
"i0_calibration_standard": null,
"description": "Individual (top) and spatially averaged (DAMFILT, middle) ab initio models are displayed.",
"experiment_description": "Synchrotron SAXS data from solutions of Halobacterium salinarum VNG0258H/RosR in 50 mM HEPES, 2 M KCl, 0.02% NaN3, pH 7 were collected 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). One solute concentration of 10.00 mg/ml was measured at 25°C. 10 successive 2 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 27.45,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 33.6,
"porod_mw_error": null,
"pddf_i0": 7.779,
"pddf_i0_error": null,
"guinier_i0": 7.88,
"guinier_i0_error": 0.019,
"pddf_rg": 2.26,
"pddf_rg_error": null,
"guinier_rg": 2.31,
"guinier_rg_error": 0.39,
"pddf_dmax": 7.5,
"pddf_dmax_error": null,
"porod_volume": 58.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 49,
"guinier_point_last": 107,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD89_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
