{ "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": [] }