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": "SASDD46",
"status": "Published",
"type_of_curve": "Single concentration",
"angular_unit": "1/nm",
"project": {
"title": "Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks.",
"publication": {
"title": "Self-Assembling Supramolecular Nanostructures Constructed from de Novo Extender Protein Nanobuilding Blocks.",
"author_list": "Kobayashi N, Inano K, Sasahara K, Sato T, Miyazawa K, Fukuma T, Hecht MH, Song C, Murata K, Arai R",
"journal": "ACS Synth Biol",
"doi": "10.1021/acssynbio.8b00007",
"pmid": "29690759",
"published_date": "2018 May 18"
},
"status": "released",
"submitted_date": "2018-04-12",
"released_date": "2018-05-07"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD46.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD46.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD46_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD46_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDD46_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD46_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDD46.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Pilatus3 2M",
"resolution": 0.172
},
"name": "Photon Factory (PF), High Energy Accelerator Research Organization (KEK)",
"city": "Tsukuba",
"country": "Japan",
"beamline_name": "BL-10C",
"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": "extender PN-Block (HL4)",
"short_name": "ePN-Block (HL4)",
"sequence": "MYGKLNKLVEHIKELLQQLNKNWHRHQGNLHDMNQQMEQLFQEFQHFMQGNQDDGKLQNMIHEMQQFMNQVDNHLQSESDTVHHFHNKLQELMNNFHHLVHRKLAEAAAKEAAAKEAAAKEAAAKAAAMYGKLNKLVEHIKELLQQLNKNWHRHQGNLHDMNQQMEQLFQEFQHFMQGNQDDGKLQNMIHEMQQFMNQVDNHLQSESDTVHHFHNKLQELMNNFHHLVHR",
"organism": "de novo protein",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 27.484,
"total_mw": 27.484,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "stopper PN-Block (WA20)",
"short_name": "sPN-Block (WA20)",
"sequence": "MYGKLNKLVEHIKELLQQLNKNWHRHQGNLHDMNQQMEQLFQEFQHFMQGNQDDGKLQNMIHEMQQFMNQVDNHLQSESDTVHHFHNKLQELMNNFHHLVHR",
"organism": "de novo protein",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": null,
"mw": 12.547,
"total_mw": 25.094,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES, 100 mM NaCl, 200 mM ArgHCl, 10% glycerol",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Artificially designed de novo protein esPN-Block (HL4) heterocomplex, e1s2 (HL4)",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Japan",
"full_name": "Shinshu University",
"webpage": "https://www.shinshu-u.ac.jp"
}
],
"contributor_name": "Ryoichi",
"contributor_surname": "Arai",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2014-12-19",
"storage_temperature": null,
"cell_temperature": 20.0,
"exposure_time": 5.0,
"number_of_frames": 30,
"wavelength": 0.1488,
"sample_detector_distance": 1.06,
"concentration_min": null,
"concentration_max": 2.6,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.112,
"s_max": 5.398,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD46_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/SASDD46_fit1_model1.pdb",
"model_mw": 37.024,
"bead_radius": 2.75,
"log": "https://www.sasbdb.org/media/log_files/esPNB_HL4_e1s2_q25_P1_q25_P1_2.log",
"symmetry": "P1",
"comment": null,
"user": 303
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD46_fit1_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.003786,
"p_value": 0.678914,
"fit_residual_plot": "SASDD46_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD46_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/esPNB_HL4_e1s2_q25_P1_q25_P1_2.log",
"software_version": null,
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD46_fit2_model1_img.png",
"software": "PyMOL",
"pdb_link": [
{
"pdb_code": "3vjf",
"ext_code": "3VJF",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": null,
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDD46_fit2_model1.pdb",
"model_mw": 52.51,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 303
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD46_fit2_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.036,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD46_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/e1s2HL4_old_1_re_2_foldit_sc_only_repack_min_200.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 an artificially designed de novo protein, esPN-Block (HL4) heterocomplex e1s2 (HL4), in 20 mM HEPES, 100 mM NaCl, 200 mM ArgHCl, 10% v/v glycerol, pH 7.5 were collected on the BL-10C beam line at the Photon Factory (PF), High Energy Acceleration Research Organization (KEK; Tsukuba, Japan) using a Pilatus 2M detector at a sample-detector distance of 1.1 m and at a wavelength of λ = 0.1488 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.60 mg/ml was measured at 20°C. 30 successive 5 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": "1/cm",
"experimental_mw": 58.1,
"experimental_mw_error": null,
"guinier_i0_mw": 58.1,
"guinier_i0_mw_error": null,
"porod_mw": null,
"porod_mw_error": null,
"pddf_i0": 0.03619,
"pddf_i0_error": 0.2663,
"guinier_i0": 0.035,
"guinier_i0_error": 0.00013,
"pddf_rg": 4.065,
"pddf_rg_error": 0.493,
"guinier_rg": 3.62,
"guinier_rg_error": 0.05,
"pddf_dmax": 15.0,
"pddf_dmax_error": null,
"porod_volume": null,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 9,
"guinier_point_last": 36,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDD46_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-06-15T13:21:24.910196+02:00",
"bragg_peak": []
}
