{ "code": "SASDVM4", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "A conformational fingerprint for amyloidogenic light chains", "publication": { "title": "A conformational fingerprint for amyloidogenic light chains", "author_list": "Paissoni C, Puri S, Broggini L, Sriramoju M, Maritan M, Russo R, Speranzini V, Ballabio F, Nuvolone M, Merlini G, Palladini G, Hsu S, Ricagno S, Camilloni C", "journal": "eLife", "doi": "10.7554/eLife.102002.3", "pmid": null, "published_date": "2025 Mar 03" }, "status": "released", "submitted_date": "2024-07-12", "released_date": "2025-02-24" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDVM4.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDVM4.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM4_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM4_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDVM4_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDVM4_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDVM4.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 6M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "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": "Immunoglobulin light chain H7", "short_name": "H7", "sequence": "QSVLTQPPSVSAAPGQKVTISCSNVGKNFVSWYQQFPGTAPKVVIYDTDKRPSDIPDRFSGSKSGTSATL\r\nDITGLQTGDEADYYCGTWDSGLNGGVFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFY\r\nPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTE\r\nCS", "organism": "Homo sapiens", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "", "mw": 22.329, "total_mw": 44.658, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": "" } ], "buffer": { "name": "20 mM TrisHCL, 150 mM NaCl", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Immunoglobulin light chain H7", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": null, "full_name": "Università degli studi di Milano", "webpage": null } ], "contributor_name": "Federico", "contributor_surname": "Ballabio", "orcid": "https://orcid.org/0000-0001-5702-3674" } ], "concentration_method": null, "concentration_unit": null, "date": "2018-05-12", "storage_temperature": 20.0, "cell_temperature": 20.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.124423, "sample_detector_distance": 2.8, "concentration_min": null, "concentration_max": 3.4, "sample_volume": null, "flow_rate": null, "s_min": 0.024, "s_max": 7.297, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDVM4_fit1_model1_img.png", "software": "MODELLER", "pdb_link": [ { "pdb_code": "5muh", "ext_code": "5MUH", "ext_type": "pdb", "difference_with_model": "identical" } ], "model_title": null, "type_of_model": "atomic", "software_version": "9.19", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDVM4_fit1_model1.pdb", "model_mw": 44.62, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 959 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDVM4_fit1_fixed_fit_img.png", "software": "Pepsi-SAXS", "chi_square_value": 2.8231, "p_value": 0.0, "fit_residual_plot": "SASDVM4_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDVM4_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/H7-H7_saxs.log", "software_version": "3", "description": "" } ], "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 immunoglobulin light chain H7 in 20 mM TrisHCL, 150 mM NaCl, pH 8 were collected on the EMBL P12 beam line at PETRA III (DESY; Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 2.8 m and at a wavelength of λ = 0.124423 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.40 mg/ml was measured at 20°C. 20 successive 0.050 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": 44.66, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 33.5, "porod_mw_error": null, "pddf_i0": 803.3, "pddf_i0_error": null, "guinier_i0": 811.431, "guinier_i0_error": null, "pddf_rg": 2.545, "pddf_rg_error": null, "guinier_rg": 2.54, "guinier_rg_error": 0.023, "pddf_dmax": 8.38, "pddf_dmax_error": null, "porod_volume": 53.7, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 36, "guinier_point_last": 174, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDVM4_datloglog_img.png", "symmetry": null, "last_modified": "2025-02-24T14:43:24.342342+01:00", "bragg_peak": [] }