{ "code": "SASDDA5", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer.", "publication": { "title": "Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer.", "author_list": "Liu J, Misra A, Reddy MVVVS, White MA, Ren G, Rudenko G", "journal": "J Mol Biol", "doi": "10.1016/j.jmb.2018.08.026", "pmid": "30193986", "published_date": "2018 Oct 19" }, "status": "released", "submitted_date": "2018-03-22", "released_date": "2018-09-10" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDDA5.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDDA5.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDA5_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDA5_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDA5_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDA5_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDDA5.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 100K", "resolution": 172.0 }, "name": "Sealy Center For Structural Biology, UTMB-G", "city": "Galveston, TX", "country": "USA", "beamline_name": "Rigaku BioSAXS-1000", "beam_geometry": null, "type_of_source": "X-ray in house", "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": "Neurexin 1a L5L6 with ss6 insert", "short_name": "L5L6ss6", "sequence": "ADPVTFKTKSSYVALATLQAYTSMHLFFQFKTTSLDGLILYNSGDGNDFIVVELVKGYLH\r\nYVFDLGNGANLIKGSSNKPLNDNQWHNVMISRDTSNLHTVKIDTKITTQITAGARNLDLK\r\nSDLYIGGVAKETYKSLPKLVHAKEGFQGCLASVDLNGRLPDLISDALFCNGQIERGCEVA\r\nLMKADLQGPSTTCQEDSCSNQGVCLQQWDGFSCDCSMTSFSGPLCNDPGTTYIFSKGGGQ\r\nITYKWPPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVG\r\nTDDIAIEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQATIII\r\nGGKEQGQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEVPS\r\nASTSHHHHHH", "organism": "Homo sapiens", "uniprot_code": "Q9ULB1", "uniprot_range_first": 904, "uniprot_range_last": 1307, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MGTALLQRGGCFLLCLSLLLLGCWAELGSGLEFPGAEGQWTRFPKWNACCESEMSFQLKT\nRSARGLVLYFDDEGFCDFLELILTRGGRLQLSFSIFCAEPATLLADTPVNDGAWHSVRIR\nRQFRNTTLFIDQVEAKWVEVKSKRRDMTVFSGLFVGGLPPELRAAALKLTLASVREREPF\nKGWIRDVRVNSSQVLPVDSGEVKLDDEPPNSGGGSPCEAGEEGEGGVCLNGGVCSVVDDQ\nAVCDCSRTGFRGKDCSQEDNNVEGLAHLMMGDQGKSKGKEEYIATFKGSEYFCYDLSQNP\nIQSSSDEITLSFKTLQRNGLMLHTGKSADYVNLALKNGAVSLVINLGSGAFEALVEPVNG\nKFNDNAWHDVKVTRNLRQHSGIGHAMVTISVDGILTTTGYTQEDYTMLGSDDFFYVGGSP\nSTADLPGSPVSNNFMGCLKEVVYKNNDVRLELSRLAKQGDPKMKIHGVVAFKCENVATLD\nPITFETPESFISLPKWNAKKTGSISFDFRTTEPNGLILFSHGKPRHQKDAKHPQMIKVDF\nFAIEMLDGHLYLLLDMGSGTIKIKALLKKVNDGEWYHVDFQRDGRSGTISVNTLRTPYTA\nPGESEILDLDDELYLGGLPENKAGLVFPTEVWTALLNYGYVGCIRDLFIDGQSKDIRQMA\nEVQSTAGVKPSCSKETAKPCLSNPCKNNGMCRDGWNRYVCDCSGTGYLGRSCEREATVLS\nYDGSMFMKIQLPVVMHTEAEDVSLRFRSQRAYGILMATTSRDSADTLRLELDAGRVKLTV\nNLDCIRINCNSSKGPETLFAGYNLNDNEWHTVRVVRRGKSLKLTVDDQQAMTGQMAGDHT\nRLEFHNIETGIITERRYLSSVPSNFIGHLQSLTFNGMAYIDLCKNGDIDYCELNARFGFR\nNIIADPVTFKTKSSYVALATLQAYTSMHLFFQFKTTSLDGLILYNSGDGNDFIVVELVKG\nYLHYVFDLGNGANLIKGSSNKPLNDNQWHNVMISRDTSNLHTVKIDTKITTQITAGARNL\nDLKSDLYIGGVAKETYKSLPKLVHAKEGFQGCLASVDLNGRLPDLISDALFCNGQIERGC\nEGPSTTCQEDSCSNQGVCLQQWDGFSCDCSMTSFSGPLCNDPGTTYIFSKGGGQITYKWP\nPNDRPSTRADRLAIGFSTVQKEAVLVRVDSSSGLGDYLELHIHQGKIGVKFNVGTDDIAI\nEESNAIINDGKYHVVRFTRSGGNATLQVDSWPVIERYPAGRQLTIFNSQATIIIGGKEQG\nQPFQGQLSGLYYNGLKVLNMAAENDANIAIVGNVRLVGEVPSSMTTESTATAMQSEMSTS\nIMETTTTLATSTARRGKPPTKEPISQTTDDILVASAECPSDDEDIDPCEPSSGGLANPTR\nAGGREPYPGSAEVIRESSSTTGMVVGIVAAAALCILILLYAMYKYRNRDEGSYHVDESRN\nYISNSAQSNGAVVKEKQPSSAKSSNKNKKNKDKEYYV", "mw": 45.5, "total_mw": 45.0, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "20 mM HEPES pH 8, 150 mM NaCl, 0.5mM CaCl2", "concentration_unit": null, "comment": "N1a Buffer", "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Neurexin 1a L5L6 with ss6 insert", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Texas, USA", "full_name": "University of Texas Medical Branch", "webpage": "http://www.bmb.utmb.edu/" } ], "contributor_name": "Mark", "contributor_surname": "White", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2016-09-26", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 10.0, "number_of_frames": 3, "wavelength": 0.15418, "sample_detector_distance": 0.4838, "concentration_min": 2.0, "concentration_max": 4.0, "sample_volume": null, "flow_rate": null, "s_min": 0.18, "s_max": 6.797, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDDA5_fit1_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDDA5_fit1_model1.pdb", "model_mw": 45.62, "bead_radius": 1.9, "log": "https://www.sasbdb.org/media/log_files/cL5s6m.log", "symmetry": "P1", "comment": null, "user": 85 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDA5_fit1_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 3.23, "p_value": 1e-06, "fit_residual_plot": "SASDDA5_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDA5_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/cL5s6m.log", "software_version": "05", "description": null }, { "models": [], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDDA5_fit2display_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 1.362, "p_value": 0.0, "fit_residual_plot": "SASDDA5_fit2display_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDDA5_fit2display.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_026_1.log", "software_version": null, "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "SAXS data from solutions of Neurexin 1a L5L6 with ss6 insert in 20 mM HEPES pH 8, 150 mM NaCl, 0.5mM CaCl2, pH 8 were collected on a Rigaku BioSAXS-1000 instrument at the Sealy Center For Structural Biology, UTMB-G (Galveston, TX, USA) using a Kratky-2D Rigaku BioSAXS-1000 detector at a sample-detector distance of 0.5 m and at a wavelength of λ = 0.15418 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 2 and 4 mg/ml were measured at 10°C. Three 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": 33.4, "experimental_mw_error": null, "guinier_i0_mw": 45.1, "guinier_i0_mw_error": 0.1, "porod_mw": 44.0, "porod_mw_error": null, "pddf_i0": 45190.0, "pddf_i0_error": 193.0, "guinier_i0": 45109.0, "guinier_i0_error": 137.0, "pddf_rg": 3.33, "pddf_rg_error": 0.02, "guinier_rg": 3.24, "guinier_rg_error": 0.1, "pddf_dmax": 12.4, "pddf_dmax_error": 0.5, "porod_volume": 70.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 10, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDDA5_datloglog_img.png", "symmetry": null, "last_modified": "2020-08-28T15:28:00.709111+02:00", "bragg_peak": [] }