{ "code": "SASDEV8", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations.", "publication": { "title": "Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations.", "author_list": "Gijsbers A, Montagut DC, Méndez-Godoy A, Altamura D, Saviano M, Siliqi D, Sánchez-Puig N", "journal": "Int J Mol Sci", "doi": "10.3390/ijms19124012", "pmid": "30545121", "published_date": "2018 Dec 12" }, "status": "released", "submitted_date": "2018-12-06", "released_date": "2018-12-14" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEV8.dat", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEV8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEV8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEV8_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEV8_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEV8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEV8.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "Diamond Light Source", "city": "Didcot", "country": "UK", "beamline_name": "B21", "beam_geometry": "1 x 5 mm", "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": "Ribosome maturation protein SDO1", "short_name": "SDO1", "sequence": "MPINQPSGQIKLTNVSLVRLKKARKRFEVACYQNKVQDYRKGIEKDLDEVLQIHQVFMNV\r\n SKGLVANKEDLQKCFGTTNVDDVIEEIMHKGEIQLSEKERQLMLNKVNNEMLTIVSAKCI\r\n NPVSKKRYPPTMIHKALQELKFSPVINKPAKLQALEAIKLLVSKQIIPIVRAKMKVKVAI\r\n SEPSRQPELIEKISKLIASSPGESTKPELDPWTCTGLIDPVNYRDLMTLCDKKGTVQVLD\r\n MAVIDNTTHN", "organism": "Saccharomyces cerevisiae", "uniprot_code": "Q07953", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MPINQPSGQIKLTNVSLVRLKKARKRFEVACYQNKVQDYRKGIEKDLDEVLQIHQVFMNV\nSKGLVANKEDLQKCFGTTNVDDVIEEIMHKGEIQLSEKERQLMLNKVNNEMLTIVSAKCI\nNPVSKKRYPPTMIHKALQELKFSPVINKPAKLQALEAIKLLVSKQIIPIVRAKMKVKVAI\nSEPSRQPELIEKISKLIASSPGESTKPELDPWTCTGLIDPVNYRDLMTLCDKKGTVQVLD\nMAVIDNTTHN", "mw": 28.283, "total_mw": 28.283, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris pH 8.0, 10% glycerol, 300 mM NaCl, 5 mM MgCl2.", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": null, "deuteration": null }, "purity_method": null, "name": "Shwachman-Bodian-Diamond Syndrome protein (yeast SDO1)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Bari, Italy", "full_name": "CNR - Institute of Crystallography, Bari, Italy", "webpage": "http://www.ba.ic.cnr.it" } ], "contributor_name": "Dritan", "contributor_surname": "Siliqi", "orcid": "https://orcid.org/0000-0003-1415-8725" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-09-21", "storage_temperature": null, "cell_temperature": 20.0, "exposure_time": 3.0, "number_of_frames": 580, "wavelength": 0.124, "sample_detector_distance": 3.0, "concentration_min": null, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.158, "s_max": 3.609, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV8_fit1_model1_img.png", "software": "MultiFoXS", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV8_fit1_model1.pdb", "model_mw": 28.29, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 396 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV8_fit1_model2_img.png", "software": "MultiFoXS", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV8_fit1_model2.pdb", "model_mw": 28.29, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 396 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV8_fit1_model3_img.png", "software": "MultiFoXS", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV8_fit1_model3.pdb", "model_mw": 28.29, "bead_radius": null, "log": null, "symmetry": null, "comment": null, "user": 396 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/multi_state_model_3_1_1_fitfoxs_img.png", "software": "FoXS", "chi_square_value": 1.292325, "p_value": 0.426822, "fit_residual_plot": "multi_state_model_3_1_1_fitfoxsresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEV8_fit1.dat", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ScÅtter", "pddf_software_version": null, "i0_calibration_standard": null, "description": "SEC-SAXS was performed at 20°C using the following parameters: Column: Shodex KW-403 ; Flow rate: 0.408 mL/min; Total acquisition time: 1740s; Sample injection concentration: 10 mg/mL; Injection volume: 45μL.", "experiment_description": "Synchrotron SAXS data from solutions of Shwachman-Bodian-Diamond Syndrome protein (yeast SDO1) in 50 mM Tris pH 8.0, 10% glycerol, 300 mM NaCl and 5 mM MgCl2., pH 8 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the B21 camera at the Diamond Light Source storage ring (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 3.0 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The data obtained through the sample elution peak (collected as 580 successive 3 second frames) were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.", "tags": [], "intensity_unit": null, "experimental_mw": 29.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 0.08047757, "pddf_i0_error": null, "guinier_i0": 0.011, "guinier_i0_error": 4e-05, "pddf_rg": 2.64, "pddf_rg_error": null, "guinier_rg": 2.74, "guinier_rg_error": 0.05, "pddf_dmax": 8.5, "pddf_dmax_error": null, "porod_volume": null, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 144, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEV8_datloglog_img.png", "symmetry": null, "last_modified": "2024-07-15T11:06:06.222393+02:00", "bragg_peak": [] }