The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"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 KIF2A",
"short_name": "Kif2A",
"sequence": "MGSSHHHHHHSSGLVPRGSSRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHRICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFTARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQVYATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAHSSRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPHTPFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKEL",
"organism": "Homo sapiens",
"uniprot_code": "O00139",
"uniprot_range_first": 153,
"uniprot_range_last": 553,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MATANFGKIQIGIYVEIKRSDGRIHQAMVTSLNEDNESVTVEWIENGDTKGKEIDLESIF\nSLNPDLVPDEEIEPSPETPPPPASSAKVNKIVKNRRTVASIKNDPPSRDNRVVGSARARP\nSQFPEQSSSAQQNGSVSDISPVQAAKKEFGPPSRRKSNCVKEVEKLQEKREKRRLQQQEL\nREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTADPIDEHRICVCVRKRPLNKKETQM\nKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYRFTARPLVET\nIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLEL\nQVYATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSC\nRTSGQTSANAHSSRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAE\nINKSLLALKECIRALGRNKPHTPFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENT\nLNTLRYANRVKELTVDPTAAGDVRPIMHHPPNQIDDLETQWGVGSSPQRDDLKLLCEQNE\nEEVSPQLFTFHEAVSQMVEMEEQVVEDHRAVFQESIRWLEDEKALLEMTEEVDYDVDSYA\nTQLEAILEQKIDILTELRDKVKSFRAALQEEEQASKQINPKRPRAL",
"mw": 47.834,
"total_mw": 47.834,
"number_molecules": 1,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Tubulin alpha-1B chain",
"short_name": "alpha tubulin",
"sequence": "MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY",
"organism": "Bos taurus",
"uniprot_code": "P81947",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK\nHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD\nRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA\nVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA\nSLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN\nQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP\nTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE\nAREDMAALEKDYEEVGVDSVEGEGEEEGEEY",
"mw": 50.151,
"total_mw": 100.302,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
},
{
"long_name": "Tubulin beta-2B chain",
"short_name": "beta 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": []
}
