{ "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": [] }