{"code":"SASDGB4","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes.","publication":{"title":"Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes.","author_list":"Das S, Malaby AW, Nawrotek A, Zhang W, Zeghouf M, Maslen S, Skehel M, Chakravarthy S, Irving TC, Bilsel O, Cherfils J, Lambright DG","journal":"Structure","doi":"10.1016/j.str.2019.09.007","pmid":"31601460","published_date":"2019 Oct 5"},"status":"released","submitted_date":"2019-08-17","released_date":"2019-09-16"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDGB4.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDGB4.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB4_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB4_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDGB4_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDGB4_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDGB4.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"MAR 165 CCD","resolution":null},"name":"Advanced Photon Source (APS), Argonne National Laboratory","city":"Lemont, IL","country":"USA","beamline_name":"BioCAT 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musculus","uniprot_code":"O08967","uniprot_range_first":14,"uniprot_range_last":390,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MDEGGGGEGGSVPEDLSLEEREELLDIRRRKKELIDDIERLKYEIAEVMTEIDNLTSVEE\nSKTTQRNKQIAMGRKKFNMDPKKGIQFLIENDLLQSSPEDVAQFLYKGEGLNKTVIGDYL\nGERDDFNIKVLQAFVELHEFADLNLVQALRQFLWSFRLPGEAQKIDRMMEAFASRYCLCN\nPGVFQSTDTCYVLSFAIIMLNTSLHNHNVRDKPTAERFITMNRGINEGGDLPEELLRNLY\nESIKNEPFKIPEDDGNDLTHTFFNPDREGWLLKLGGRVKTWKRRWFILTDNCLYYFEYTT\nDKEPRGIIPLENLSIREVEDPRKPNCFELYNPSHKGQVIKACKTEADGRVVEGNHVVYRI\nSAPSPEEKEEWMKSIKASISRDPFYDMLATRKRRIANKK","mw":45.153,"total_mw":90.306,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"20 mM Tris, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, 5% glycerol, 0.001 mM insitol 1,3,4,5-tetrakis phosphate","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"Active dimer of truncated 6xHis Cytohesin-3 (Grp1, amino acids 14-390) with Inositol 1,3,4,5-tetrakis phosphate (antiparallel CORAL and MultiFoXS models)","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"UMASS","address":"Worcester, MA, USA","full_name":"UMASS Medical School","webpage":"https://www.umassmed.edu/"}],"contributor_name":"David","contributor_surname":"Lambright","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2013-11-15","storage_temperature":null,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":126,"wavelength":0.10332,"sample_detector_distance":2.5,"concentration_min":null,"concentration_max":10.0,"sample_volume":100.0,"flow_rate":0.25,"s_min":0.069,"s_max":3.162,"total_exposure_time":null,"seccolumn":14},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGB4_fit1_model1_img.png","software":"CORAL","pdb_link":[{"pdb_code":"2r09","ext_code":"2R09","ext_type":"pdb","difference_with_model":"derived"}],"model_title":null,"type_of_model":"mix","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGB4_fit1_model1.pdb","model_mw":93.29,"bead_radius":1.9,"log":"https://www.sasbdb.org/media/log_files/coral_e1fNQT7.log","symmetry":"P1","comment":"Derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil","user":241}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGB4_fit1_fixed_fit_img.png","software":"CORAL","chi_square_value":1.4,"p_value":0.015784,"fit_residual_plot":"SASDGB4_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDGB4_fit1.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/coral_8dh0Za4.log","software_version":"CORAL05","description":"Fit for CORAL model derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil"},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGB4_fit2_model1_img.png","software":"MultiFoXS","pdb_link":[{"pdb_code":"2r09","ext_code":"2R09","ext_type":"pdb","difference_with_model":"derived"}],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGB4_fit2_model1.pdb","model_mw":91.5,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/ensembles_size_3_tSjM7yn.txt","symmetry":"P1","comment":"Derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil","user":241},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGB4_fit2_model2_img.png","software":"MultiFoXS","pdb_link":[{"pdb_code":"2r09","ext_code":"2R09","ext_type":"pdb","difference_with_model":"identical"}],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGB4_fit2_model2.pdb","model_mw":91.5,"bead_radius":null,"log":null,"symmetry":"P1","comment":"Derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil","user":241},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDGB4_fit2_model3_img.png","software":"MultiFoXS","pdb_link":[{"pdb_code":"2r09","ext_code":"2R09","ext_type":"pdb","difference_with_model":"derived"}],"model_title":null,"type_of_model":"atomic","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDGB4_fit2_model3.pdb","model_mw":91.5,"bead_radius":null,"log":"https://www.sasbdb.org/media/log_files/ensembles_size_3_Wj2dooP.txt","symmetry":"P1","comment":"Derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil","user":241}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDGB4_fit2_fitfoxs_img.png","software":"MultiFoXS","chi_square_value":1.021347,"p_value":0.003902,"fit_residual_plot":"SASDGB4_fit2_fitfoxsresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDGB4_fit2.dat","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/ensembles_size_3_UIBC4WJ.txt","software_version":null,"description":"Fit for MultiFoXS ensemble with 3 models derived from Grp1 63-399 (2R09) and a canonical antiparallel coiled coil"}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"The protein was equilibrated with a 1.2 molar excess of inositol 1,3,4,5-tetrakis phosphate (IP4) and concentrated to 10 mg/ml prior to injection.","experiment_description":"Synchrotron SAXS data from solutions of the active dimer of truncated Cytohesin-3 (Grp1, amino acids 14-390) in 20 mM Tris, 150 mM NaCl, 2 mM MgCl2, 0.1% 2-mercaptoethanol, 5% glycerol, 0.001 mM insitol 1,3,4,5-tetrakis phosphate, pH 8 were collected on the BioCAT 18ID beam line at the Advanced Photon Source (APS), Argonne National Laboratory (Lemont, IL, USA) using a MAR 165 CCD detector at a sample-detector distance of 2.5 m and at a wavelength of λ = 0.10332 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 100.00 μl sample at 10 mg/ml was injected at a 0.25 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 20°C. SAXS data sets were acquired with 1 s exposures at 5 s intervals during the elution. Raw SAXS images were radially averaged on a log scale over the s range 0.0621-3.33 nm-1 and normalized by the incident beam intensity. The protein scattering profile was reconstructed by singular value decomposition and linear combination (SVD-LC) as described in Malaby et al. (2015) Methods for analysis of size-exclusion chromatography-small angle X-ray scattering and reconstruction of protein scattering. J Appl Crystallogr 48: 1102-1113.","tags":[],"intensity_unit":"arbitrary","experimental_mw":86.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":1.03,"pddf_i0_error":0.005,"guinier_i0":1.02,"guinier_i0_error":0.002,"pddf_rg":5.43,"pddf_rg_error":0.14,"guinier_rg":5.06,"guinier_rg_error":0.04,"pddf_dmax":25.7,"pddf_dmax_error":0.1,"porod_volume":168.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":1,"guinier_point_last":20,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDGB4_datloglog_img.png","symmetry":null,"last_modified":"2024-10-17T15:36:28.559854+02:00","bragg_peak":[]}