{"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 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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":[]}