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{
"code": "SASDE55",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.",
"publication": {
"title": "Size-exclusion chromatography small-angle X-ray scattering of water soluble proteins on a laboratory instrument.",
"author_list": "Bucciarelli S, Midtgaard SR, Nors Pedersen M, Skou S, Arleth L, Vestergaard B",
"journal": "J Appl Crystallogr",
"doi": "10.1107/S1600576718014462",
"pmid": "30546289",
"published_date": "2018 Dec 1"
},
"status": "released",
"submitted_date": "2018-09-29",
"released_date": "2018-11-11"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDE55.d",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDE55.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE55_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE55_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDE55_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDE55_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDE55.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "pixel counting",
"name": "Pilatus3 R 300K",
"resolution": 172.0
},
"name": "University of Copenhagen, Department of Drug Design and Pharmacology",
"city": "Copenhagen",
"country": "Denmark",
"beamline_name": "Xenocs BioXolver L with MetalJet",
"beam_geometry": null,
"type_of_source": "X-ray in house",
"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": "HAF",
"sequence": "SSQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKRE\r\nGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSAQ\r\nADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLKHD",
"organism": "Equus caballus",
"uniprot_code": "P02791",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "24-mer",
"molecular_type": "protein",
"uniprot_sequence": "MSSQIRQNYSTEVEAAVNRLVNLYLRASYTYLSLGFYFDRDDVALEGVCHFFRELAEEKR\nEGAERLLKMQNQRGGRALFQDLQKPSQDEWGTTLDAMKAAIVLEKSLNQALLDLHALGSA\nQADPHLCDFLESHFLDEEVKLIKKMGDHLTNIQRLVGSQAGLGEYLFERLTLKHD",
"mw": 19.846,
"total_mw": 476.304,
"number_molecules": 24,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "PBS",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.4,
"deuteration": null
},
"purity_method": null,
"name": "Apoferritin monomer from in-house SEC-SAXS",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Copenhagen, Denmark",
"full_name": "University of Copenhagen",
"webpage": "http://www.ku.dk/"
}
],
"contributor_name": "Saskia",
"contributor_surname": "Bucciarelli",
"orcid": "https://orcid.org/0000-0001-7612-223X"
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2018-01-24",
"storage_temperature": null,
"cell_temperature": 23.0,
"exposure_time": 30.0,
"number_of_frames": 11,
"wavelength": 0.134,
"sample_detector_distance": null,
"concentration_min": null,
"concentration_max": 3.7,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.075,
"s_max": 5.022,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE55_fit1_model1_img.png",
"software": "PDB (Protein Data Bank)",
"pdb_link": [
{
"pdb_code": "1ies",
"ext_code": "1IES",
"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/SASDE55_fit1_model1.pdb",
"model_mw": 478.4,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 365
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/1ies_full00_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 19.151,
"p_value": 0.000263,
"fit_residual_plot": "1ies_full00_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDE55_fit1.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/1ies_full00.log",
"software_version": null,
"description": "Instrumental smearing was not taken into account for the fitting."
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDE55_fit2_model1_img.png",
"software": "DAMFILT",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
"software_version": "5.0",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDE55_fit2_model1.pdb",
"model_mw": 370.098,
"bead_radius": 4.5,
"log": "https://www.sasbdb.org/media/log_files/merged_Ferritin_11p1mgmL_damsel.log",
"symmetry": "P1",
"comment": null,
"user": 365
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/merged_Ferritin_11p1mgmL_01_fit_img.png",
"software": "DAMMIF",
"chi_square_value": 14.395,
"p_value": 0.089007,
"fit_residual_plot": "merged_Ferritin_11p1mgmL_01_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDE55_fit2.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/merged_Ferritin_11p1mgmL_01.log",
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "BayesApp",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": "The HAF sample (500 microlitres at 11.1 mg/ml) was injected onto a GE Healthcare S200 Increase 10/300 (24 ml) column at a flow rate of 0.1 ml/min 23°C. A total of 100 x 30 second SAXS data frames were recorded throughout the HAF elution at a sample-detector distance of 0.654 m and 110 x 30 second SAXS data frames at a sample-detector distance of 1.507 m. After background solvent corrections, SEC-SAXS data frames 65-75 and 66-76, respectively, corresponding to monomeric HAF, were scaled, averaged, binned logarithmically and merged to produce the data displayed in this entry. Additional files, including plots of the selected frames and of I(0), HPLC and exposure cell UV traces and Rg vs. time (determined by AUTORG) in both sample-detector settings are included in the additional files of the full entry zip archive.",
"experiment_description": "SAXS data from solutions of Apoferritin monomer from in-house SEC-SAXS in PBS, pH 7.4 were collected on a Xenocs BioXolver L instrument at the Copenhagen University, Department of Drug Design and Pharmacology (Copenhagen, Denmark) using a 20Hz Pilatus 300K detector at a wavelength of λ = 0.134 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle).",
"tags": [],
"intensity_unit": "arbitrary",
"experimental_mw": 437.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 437.0,
"porod_mw_error": null,
"pddf_i0": 2.3,
"pddf_i0_error": 0.0,
"guinier_i0": 2.248,
"guinier_i0_error": 0.018,
"pddf_rg": 5.221,
"pddf_rg_error": 0.004,
"guinier_rg": 5.13,
"guinier_rg_error": 0.057,
"pddf_dmax": 12.28,
"pddf_dmax_error": 0.39,
"porod_volume": 685.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 8,
"guinier_point_last": 19,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDE55_datloglog_img.png",
"symmetry": null,
"last_modified": "2019-12-06T13:07:15.624532+01:00",
"bragg_peak": []
}
