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{
"code": "SASDWW6",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Structural insights into the nature of static and dynamic apoferritin dimers",
"publication": null,
"status": "released",
"submitted_date": "2025-01-28",
"released_date": "2026-01-28"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWW6.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWW6.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWW6_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWW6_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWW6_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWW6_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWW6.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "Shanghai Synchrotron Radiation Facility (SSRF)",
"city": "Shanghai",
"country": "China",
"beamline_name": "BL19U2",
"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": "Ferritin light chain",
"short_name": "Apoferritin dimer",
"sequence": "SSQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKREGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLKHD",
"organism": "Equus caballus",
"uniprot_code": "P02791",
"uniprot_range_first": 2,
"uniprot_range_last": 175,
"oligomerization": "other",
"molecular_type": "protein",
"uniprot_sequence": "MSSQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKR\nEGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSA\nQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLKHD",
"mw": 19.846,
"total_mw": 952.608,
"number_molecules": 48,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "137 mM NaCl, 2.7 mM KCl, 10 mM phosphate buffer, 0.9 mM CaCl2, 0.5 mM MgCl2",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "SEC-SAXS data for the total dimer (2 x 24mer) fraction of horse spleen apoferritin",
"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": "University of Groningen",
"webpage": null
}
],
"contributor_name": "Aleksei",
"contributor_surname": "Tsarenko",
"orcid": "https://orcid.org/0000-0002-4221-3317"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-05-24",
"storage_temperature": 4.0,
"cell_temperature": 20.0,
"exposure_time": 1.0,
"number_of_frames": 40,
"wavelength": 0.1033,
"sample_detector_distance": 2.696,
"concentration_min": null,
"concentration_max": 23.5,
"sample_volume": 20.0,
"flow_rate": 0.5,
"s_min": 0.058,
"s_max": 4.068,
"total_exposure_time": null,
"seccolumn": 5
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWW6_fit1_model1_img.png",
"software": "Chimera",
"pdb_link": [
{
"pdb_code": "2w0o",
"ext_code": "2W0O",
"ext_type": "pdb",
"difference_with_model": "identical"
}
],
"model_title": null,
"type_of_model": "atomic",
"software_version": "1.14",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWW6_fit1_model1.pdb",
"model_mw": 929.0,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1173
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWW6_fit1_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.22,
"p_value": 0.0,
"fit_residual_plot": "SASDWW6_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWW6_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/crystal-contacts__dimer00_6Y82XzE.log",
"software_version": "3.0",
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWW6_fit2_model1_img.png",
"software": "Chimera",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "1.14",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWW6_fit2_model1.pdb",
"model_mw": 930.7,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1173
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWW6_fit2_fixed_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 1.236,
"p_value": 0.0,
"fit_residual_plot": "SASDWW6_fit2_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWW6_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/H-cys90--H-cys90_dimer00_hZeOa3x.log",
"software_version": "3.0",
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "The preparation and analysis of horse spleen apoferritin were conducted to isolate its monomeric (24mer) and dimeric (2 x 24mer) forms and enable detailed structural characterization.\r\n Sample Preparation:\r\nAn apoferritin stock solution (horse spleen apoferritin, purchased from Sigma-Aldrich, Merck KGaA, Germany, supplied with 50% v/v glycerol) was centrifuged at 10,000 rcf for 10 minutes.\r\n Size Exclusion Chromatography and SAXS Analysis:\r\nApproximately 20 μl of the supernatant were loaded onto a Superose 6 Increase 10/300 column (GE Healthcare), equilibrated in DPBS buffer (137 mM NaCl, 2.7 mM KCl, 10 mM phosphate buffer, pH 7.4, 0.9 mM CaCl2, 0.5 mM MgCl2). The flow rate was set at 0.5 ml/min. SAXS frames corresponding to the dimeric (2 x 24mer) fraction of apoferritin (elution volume range: 12.9–13.25 ml) with a constant Rg value were selected for further analysis.",
"experiment_description": "Synchrotron SAXS data from solutions of horse spleen apoferritin in 137 mM NaCl, 2.7 mM KCl, 10 mM phosphate buffer, 0.9 mM CaCl2, 0.5 mM MgCl2, pH 7.4 were collected on the BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF; Shanghai, China) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.1033 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 20.00 μl sample at 23.5 mg/ml was injected at a 0.50 ml/min flow rate onto a GE Superose 6 Increase 10/300 column at 20°C. 40 successive 1 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": 952.63,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 1446.9,
"porod_mw_error": null,
"pddf_i0": 0.01654,
"pddf_i0_error": 0.0002,
"guinier_i0": 0.0163419,
"guinier_i0_error": 0.0002,
"pddf_rg": 7.98,
"pddf_rg_error": 0.1,
"guinier_rg": 7.717,
"guinier_rg_error": 0.2,
"pddf_dmax": 25.0,
"pddf_dmax_error": null,
"porod_volume": 1750.59,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 1,
"guinier_point_last": 32,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDWW6_datloglog_img.png",
"symmetry": null,
"last_modified": "2026-02-04T12:12:11.021690+01:00",
"bragg_peak": []
}
