{ "code": "SASDAG7", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/nm", "project": { "title": "Molecular mechanism for the action of the anti-CD44 monoclonal antibody MEM-85.", "publication": { "title": "Molecular mechanism for the action of the anti-CD44 monoclonal antibody MEM-85.", "author_list": "Škerlová J, Král V, Kachala M, Fábry M, Bumba L, Svergun DI, Tošner Z, Veverka V, Řezáčová P", "journal": "J Struct Biol", "doi": "10.1016/j.jsb.2015.06.005", "pmid": "26066970", "published_date": "2015 Aug" }, "status": "released", "submitted_date": null, "released_date": "2015-07-30" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDAG7.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDAG7.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAG7_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAG7_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDAG7_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDAG7_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDAG7.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "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": "Hyaluronate binding domain of CD44 antigen", "short_name": "CD44 HABD", "sequence": "SNAASQIDLNITCRFAGVFHVEKNGRYSISRTEAADLCKAFNSTLPTMAQMEKALSIGFE\r\nTCRYGFIEGHVVIPRIHPNSICAANNTGVYILTSNTSQYDTYCFNASAPPEEDCTSVTDL\r\nPNAFDGPITITIVNRDGTRYVQKGEYRTNPEDIYPSNPTDDDV\r\n", "organism": "Homo sapiens", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 17.9, "total_mw": 17.9, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "Single-chain Variable Fragment of Antibody MEM-85", "short_name": "scFv MEM-85", "sequence": "EVQLQESGPGLVAPSQSLSITCTVSGFSLTNYGVHWVRQPPGKGLEWLGVIWAGGSTNYN\r\nSALMSRLSISKDNSKSQVFLKMNSLQTDDTAMYYCARDGARAMDYWGQGTTVTVSGGGGS\r\nGGGGSGGGGSGGGGSDIVMSQSPSSLAVSVGEKVTVSCKSSQSLLYSSNQKNYLAWYQQK\r\nPGQSPKLLISWASTRESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQSYSYPWTFG\r\nGGTKLEIKREQKLISEEDLNGTHHHHH", "organism": "Mus musculus", "uniprot_code": null, "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": null, "mw": 28.5, "total_mw": 28.5, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "PBS", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": 7.0, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "CD44 HABD scFv MEM-85 complex", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Michael", "contributor_surname": "Kachala", "orcid": null } ], "concentration_method": null, "concentration_unit": "mg/ml", "date": "2013-10-31", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.12, "sample_detector_distance": 3.1, "concentration_min": 1.3, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.2, "s_max": 4.488, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAG7_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDAG7_fit1_model1.pdb", "model_mw": 37.545, "bead_radius": 2.5, "log": null, "symmetry": "P1", "comment": "", "user": 3 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAG7_fit1_fit_img.png", "software": null, "chi_square_value": 2.46, "p_value": 0.0, "fit_residual_plot": "SASDAG7_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAG7_fit1.fir", "fit_log": null, "software_version": null, "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDAG7_fit2_model1_img.png", "software": "SASREF", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDAG7_fit2_model1.pdb", "model_mw": 40.71, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 3 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDAG7_fit2_fit_img.png", "software": null, "chi_square_value": 1.24, "p_value": 0.0, "fit_residual_plot": "SASDAG7_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDAG7_fit2.fit", "fit_log": null, "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": null, "i0_calibration_standard": "BSA", "description": null, "experiment_description": null, "tags": [], "intensity_unit": null, "experimental_mw": 44.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 8363.0, "pddf_i0_error": 135.0, "guinier_i0": 8235.0, "guinier_i0_error": 83.0, "pddf_rg": 2.81, "pddf_rg_error": 0.05, "guinier_rg": 2.69, "guinier_rg_error": 0.14, "pddf_dmax": 9.4, "pddf_dmax_error": 1.0, "porod_volume": 57.0, "porod_volume_error": 200.0, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": null, "guinier_point_last": null, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDAG7_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }