{"code":"SASDCR9","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/A","project":{"title":"Ternary complex of Kif2A-bound tandem tubulin heterodimers represents a kinesin-13-mediated microtubule depolymerization reaction intermediate.","publication":{"title":"Ternary complex of Kif2A-bound tandem tubulin heterodimers represents a kinesin-13-mediated microtubule depolymerization reaction intermediate.","author_list":"Trofimova D, Paydar M, Zara A, Talje L, Kwok BH, Allingham JS","journal":"Nat Commun","doi":"10.1038/s41467-018-05025-7","pmid":"29980677","published_date":"2018 Jul 6"},"status":"released","submitted_date":"2017-11-28","released_date":"2018-05-15"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDCR9.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDCR9.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCR9_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCR9_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCR9_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCR9_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDCR9.sascif","experiment":{"instrument":{"detector":{"type":"CCD","name":"Finger Lakes CCD","resolution":0.0},"name":"Cornell High Energy Synchrotron Source (CHESS)","city":"Ithaca, NY","country":"USA","beamline_name":"G1","beam_geometry":"","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":"Designed Ankyrin Repeat Protein D1","short_name":"DARPin D1","sequence":"MGSHHHHHHGSDLGKKLLEAARAGQDDEVRILMANGADVNATDASGLTPLHLAATYGHLEIVEVLLKHGADVNAIDIMGSTPLHLAALIGHLEIVEVLLKHGADVNAVDTWGDTPLHLAAIMGHLEIVEVLLKHGADVNAQDKFGKTAFDISIDNGNEDLAEILQKLN","organism":"synthetic construct","uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":null,"mw":17.886,"total_mw":17.886,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null},{"long_name":"Kinesin-like protein 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tubulin","sequence":"MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYVPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVVEPYNATLSVHQLVENTDETYSIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMMAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATADEQGEFEEEEGEDEA","organism":"Bos taurus","uniprot_code":"Q6B856","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"dimer","molecular_type":"protein","uniprot_sequence":"MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEATGNKYV\nPRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV\nRKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVMPSPKVSDTVV\nEPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL\nRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDSKNMM\nAACDPRHGRYLTVAAIFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG\nLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS\nEYQQYQDATADEQGEFEEEEGEDEA","mw":49.936,"total_mw":99.872,"number_molecules":2,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"HEPES 20 mM, MgCl2 1mM, NaCl 150mM","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.2,"deuteration":null},"purity_method":null,"name":"Kif2A-tubulin-DARP complex in the presence of AMP-PNP","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Kingston, ON, Canada","full_name":"Queen's University","webpage":"http://www.queensu.ca/"}],"contributor_name":"Daria","contributor_surname":"Trofimova","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2016-05-16","storage_temperature":4.0,"cell_temperature":22.0,"exposure_time":2.0,"number_of_frames":1200,"wavelength":0.1267,"sample_detector_distance":1.47,"concentration_min":null,"concentration_max":3.7,"sample_volume":null,"flow_rate":null,"s_min":0.086,"s_max":2.735,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDCR9_fit1_model1_img.png","software":"DAMMIF","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDCR9_fit1_model1.pdb","model_mw":240.0,"bead_radius":4.1,"log":null,"symmetry":"P1","comment":null,"user":260}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCR9_fit1_fit_img.png","software":"DAMMIF","chi_square_value":1.02,"p_value":0.761362,"fit_residual_plot":"SASDCR9_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDCR9_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/S_A_Kif2ATubDARPin_A4_64_001_0434_big_comp_subst_01_qE84UBp.log","software_version":null,"description":null},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDCR9_fit2_model1_img.png","software":"PDB (Protein Data Bank)","pdb_link":[{"pdb_code":"6bbn","ext_code":"6BBN","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/SASDCR9_fit2_model1.pdb","model_mw":253.4,"bead_radius":1.9,"log":null,"symmetry":"P21","comment":null,"user":260}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCR9_fit2_fit_img.png","software":"CRYSOL","chi_square_value":1.087,"p_value":0.600511,"fit_residual_plot":"SASDCR9_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDCR9_fit2.fit","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/Kif2A_TubDar_Final00.log","software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":null,"i0_calibration_standard":null,"description":"For the SEC-SAXS analysis, a mixture of Kif2A, tubulin and DARPin was passed continuously through an X-ray sample cell via an in-line size exclusion column (GE Superdex 200 10/300 GL) at a flow rate of 1 ml/min. The column was pre-equilibrated with running buffer consisting of 20 mM HEPES, 150 mM NaCl, 1 mM MgCl2 pH 7.2. The protein sample was prepared at 25 μM tubulin, 27 μM DARP in and 20 μM Kif2A and injected into a 100 μL loop. Approximately 1200 two-second exposures were collected per sample, and 100 buffer profiles preceding the elution peaks were averaged and used for background subtraction.","experiment_description":"Synchrotron SAXS data from solutions of Kif2A-tubulin-DARPin complex in presence of AMP-PNP in 20 mM HEPES, 1 mM MgCl2, 150 mM NaCl, pH 7.2 were collected at the BioSAXS G1 beam line at the Cornell High Energy Synchrotron Source (CHESS; Ithaca, NY, USA) using a CCD Finger Lakes CCD detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.1267 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). 1200 successive 2 second frames were collected using size exclusion chromatography SAXS (SEC-SAXS; 3.70 mg/ml sample injection at 22°C).","tags":[],"intensity_unit":"arbitrary","experimental_mw":258.5,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":279.7,"porod_mw_error":null,"pddf_i0":0.0298,"pddf_i0_error":0.00029,"guinier_i0":0.02949,"guinier_i0_error":0.0002,"pddf_rg":5.6,"pddf_rg_error":0.03,"guinier_rg":5.41,"guinier_rg_error":0.05,"pddf_dmax":19.5,"pddf_dmax_error":null,"porod_volume":374.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":4,"guinier_point_last":26,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDCR9_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}