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{
"code": "SASDWK2",
"status": "Published",
"type_of_curve": "SEC-SAS",
"angular_unit": "1/A",
"project": {
"title": "Small-angle X-ray scattering of engineered antigen-binding fragments: the case of glycosylated Fab from the Mannitou IgM antibody.",
"publication": {
"title": "Small-angle X-ray scattering of engineered antigen-binding fragments: the case of glycosylated Fab from the Mannitou IgM antibody.",
"author_list": "Semwal S, Karamolegkou M, Flament S, Raouraoua N, Verstraete K, Thureau A, Wien F, Bray F, Savvides SN, Bouckaert J",
"journal": "Acta Crystallogr F Struct Biol Commun",
"doi": "10.1107/S2053230X24012159",
"pmid": "39718025",
"published_date": "2025 Jan 1"
},
"status": "released",
"submitted_date": "2024-11-25",
"released_date": "2024-12-30"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDWK2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDWK2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWK2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWK2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDWK2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDWK2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDWK2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": null,
"name": "Eiger 4M",
"resolution": 75.0
},
"name": "SOLEIL",
"city": "Saint-Aubin",
"country": "France",
"beamline_name": "SWING",
"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": "IgM Mannitou Fab Heavy Chain",
"short_name": "Fab Monomer",
"sequence": "EVKLLESGGGLVQPGGSLKLSCAASGFDFSTYWMSWVRQAPGKGLEWIGEINPDSSTINYTPSLKDKFIISRDNAKNTLYLQMSKVRSEDSVLYYCVRPGTWGYFDYWGQGTTLTVSSESQSFPNVFPLVSCESPLSDKNLVAMGCLARDFLPSTISFTWNYQNNTEVIQGIRTFPTLRTGGKYLATSQVLLSPKSILEGSDEYLVCKIHYGGKNRDLHVPIPHHHHHH",
"organism": "Mus musculus",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "",
"mw": 25.574,
"total_mw": 25.574,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": "The protein construct used for SAXS contains an additional C-terminal polyhistidine tag."
},
{
"long_name": "IgM Mannitou Fab Light Chain",
"short_name": null,
"sequence": "DVVVTQTPLSLPVSFGDQASISCRSSQSLVNSYGSTYLSWYLHRPGQSPQLLIYGISNRFSGVPDRFSGSGSGTDFTLTIRTIKPEDLGMYYCLQGTHQPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRKEC",
"organism": "Mus musculus",
"uniprot_code": null,
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "",
"mw": 24.187,
"total_mw": 24.187,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": ""
}
],
"buffer": {
"name": "20 mM HEPES, 300 mM NaCl",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Mannitou IgM Fab Monomer",
"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 Lille",
"webpage": null
}
],
"contributor_name": "Shubham",
"contributor_surname": "Semwal",
"orcid": ""
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2024-06-05",
"storage_temperature": 4.0,
"cell_temperature": 15.0,
"exposure_time": 0.99,
"number_of_frames": 580,
"wavelength": 0.1033,
"sample_detector_distance": 2.0,
"concentration_min": null,
"concentration_max": 9.2,
"sample_volume": 50.0,
"flow_rate": 0.3,
"s_min": 0.041,
"s_max": 5.511,
"total_exposure_time": null,
"seccolumn": 10
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWK2_fit1_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWK2_fit1_model1.pdb",
"model_mw": 51.82,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": "Alphafold2 based model with glycan added based on MS results using GlycoSHIELD software.",
"user": 1130
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWK2_fit1_fixed_fit_img.png",
"software": "FoXS",
"chi_square_value": 2.797612,
"p_value": 0.0,
"fit_residual_plot": "SASDWK2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWK2_fit1.fit",
"fit_log": null,
"software_version": null,
"description": ""
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDWK2_fit2_model1_img.png",
"software": "AlphaFold",
"pdb_link": [],
"model_title": null,
"type_of_model": "atomic",
"software_version": "2",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDWK2_fit2_model1.pdb",
"model_mw": 51.82,
"bead_radius": null,
"log": null,
"symmetry": null,
"comment": null,
"user": 1130
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDWK2_fit2_fitfoxs_img.png",
"software": "MultiFoXS",
"chi_square_value": 2.798367,
"p_value": 0.0,
"fit_residual_plot": "SASDWK2_fit2_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDWK2_fit2.dat",
"fit_log": null,
"software_version": null,
"description": ""
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": null,
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of mannitou IgM Fab in 20 mM HEPES, 300 mM NaCl, pH 7.5 were collected on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 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 50.00 μl sample at 9.2 mg/ml was injected at a 0.30 ml/min flow rate onto a Agilent Bio SEC-3, 300 Å column at 15°C. 580 successive 0.990 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": 53.1,
"experimental_mw_error": null,
"guinier_i0_mw": 53.0,
"guinier_i0_mw_error": null,
"porod_mw": 50.0,
"porod_mw_error": null,
"pddf_i0": 93.02,
"pddf_i0_error": 0.103,
"guinier_i0": 92.2411,
"guinier_i0_error": null,
"pddf_rg": 2.85,
"pddf_rg_error": 0.009,
"guinier_rg": 2.77,
"guinier_rg_error": 0.074,
"pddf_dmax": 12.5,
"pddf_dmax_error": 0.09,
"porod_volume": 74.0,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 40,
"guinier_point_last": 85,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDWK2_datloglog_img.png",
"symmetry": null,
"last_modified": "2024-12-30T08:16:44.790607+01:00",
"bragg_peak": []
}
