{ "code": "SASDD23", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition.", "publication": { "title": "The structure of SALM5 suggests a dimeric assembly for the presynaptic RPTP ligand recognition.", "author_list": "Karki S, Paudel P, Sele C, Shkumatov AV, Kajander T", "journal": "Protein Eng Des Sel", "doi": "10.1093/protein/gzy012", "pmid": "29897575", "published_date": "2018 Jun 12" }, "status": "released", "submitted_date": "2018-01-11", "released_date": "2018-06-13" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDD23.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDD23.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD23_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDD23_kratky_img.png", 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"MEKFLFYLFLIGIAVRAQICPKRCVCQILSPNLATLCAKKGLLFVPPNIDRRTVELRLAD\nNFVTNIKRKDFANMTSLVDLTLSRNTISFITPHAFADLRNLRALHLNSNRLTKITNDMFS\nGLSNLHHLILNNNQLTLISSTAFDDVFALEELDLSYNNLETIPWDAVEKMVSLHTLSLDH\nNMIDNIPKGTFSHLHKMTRLDVTSNKLQKLPPDPLFQRAQVLATSGIISPSTFALSFGGN\nPLHCNCELLWLRRLSREDDLETCASPALLTGRYFWSIPEEEFLCEPPLITRHTHEMRVLE\nGQRATLRCKARGDPEPAIHWISPEGKLISNATRSLVYDNGTLDILITTVKDTGAFTCIAS\nNPAGEATQTVDLHIIKLPHLLNSTNHIHEPDPGSSDISTSTKSGSNASSSNGDTKMSQDK\nIVVAEATSSTALLKFNFQRNIPGIRMFQIQYNGTYDDTLVYRMIPPTSKTFLVNNLASGT\nMYDLCVLAIYDDGITSLTATRVVGCIQFTTEQDYVRCHFMQSQFLGGTMIIIIGGIIVAS\nVLVFIIILMIRYKVCNNNGQHKVTKVSNVYSQTNGAQMQGCSVTLPQSMSKQAMGHEENA\nQCCKVASDNAIQSSETCSSQDSSTTTSALPPTWTSSAPVSQKQKRKTGTKPSAEPQSEAV\nTNVESQNTNRNNSTALQLASCPPDSVTEGPTSQRAHTKPNALLTNVDQNVQETQRLESI", "mw": 41.018, "total_mw": 82.036, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "30 mM Tris-Cl, 150 mM NaCl, 3% glycerol", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Leucine-rich repeat and fibronectin type-III domain-containing protein 5: Fragment SALM5 LRR-Ig", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "VUB", "address": "Pleinlaan 2 1050 Brussel ", "full_name": "Vrije Universiteit Brussel", "webpage": "http://www.vub.ac.be/" } ], "contributor_name": "Alexander", "contributor_surname": "Shkumatov", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-06-08", "storage_temperature": 15.0, "cell_temperature": 15.0, "exposure_time": 10.0, "number_of_frames": 18, "wavelength": 0.1005, "sample_detector_distance": 4.036, "concentration_min": 1.0, "concentration_max": 5.0, "sample_volume": null, "flow_rate": null, "s_min": 0.222, "s_max": 3.501, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "r9684", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD23_fit1_model1.pdb", "model_mw": 90.355, "bead_radius": 3.25, "log": "https://www.sasbdb.org/media/log_files/refine_QIuM8uc.log", "symmetry": "P1", "comment": "averaged (damstart.pdb) refined model", "user": 104 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD23_fit1_fixed_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.29, "p_value": 0.0, "fit_residual_plot": "SASDD23_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD23_fit1.fir", "fit_log": null, "software_version": "r9684", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_fit2_model1_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "r9684", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD23_fit2_model1.pdb", "model_mw": 87.21, "bead_radius": 1.9, "log": null, "symmetry": "P2", "comment": null, "user": 104 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_fit2_model2_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "r9684", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD23_fit2_model2.pdb", "model_mw": 87.21, "bead_radius": 1.9, "log": null, "symmetry": "P2", "comment": null, "user": 104 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_fit2_model3_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "r9684", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD23_fit2_model3.pdb", "model_mw": 87.21, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 104 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_fit2_model4_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "r9684", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD23_fit2_model4.pdb", "model_mw": 87.21, "bead_radius": 1.9, "log": null, "symmetry": "P2", "comment": null, "user": 104 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDD23_fit2_model5_img.png", "software": "EOM/RANCH", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "r9684", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDD23_fit2_model5.pdb", "model_mw": 87.21, "bead_radius": 1.9, "log": null, "symmetry": "P2", "comment": null, "user": 104 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDD23_fit2_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 1.226, "p_value": 0.0, "fit_residual_plot": "SASDD23_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDD23_fit2.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_005_1.log", "software_version": "r9684", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of Leucine-rich repeat and fibronectin type-III domain-containing protein 5 (fragment SALM5 (LRR-Ig)) in 30 mM Tris-Cl, 150 mM NaCl, 3% v/v glycerol, pH 7.5, were collected on the B21 beam line at the Diamond Light Source storage ring (Oxfordshire, UK) using a Pilatus 2M detector at a sample-detector distance of 4.0 m and at a wavelength of λ = 0.1005 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 5 mg/ml were measured at 15°C. 18 successive 10 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. The low angle data collected at lower concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 101.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 91.1, "porod_mw_error": null, "pddf_i0": 0.00669, "pddf_i0_error": 0.0001, "guinier_i0": 0.006724, "guinier_i0_error": 3e-05, "pddf_rg": 3.65, "pddf_rg_error": 0.01, "guinier_rg": 3.63, "guinier_rg_error": 0.02, "pddf_dmax": 13.5, "pddf_dmax_error": 1.0, "porod_volume": 155.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 2, "guinier_point_last": 50, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDD23_datloglog_img.png", "symmetry": null, "last_modified": "2020-08-28T15:27:46.196867+02:00", "bragg_peak": [] }