{ "code": "SASDC22", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/nm", "project": { "title": "Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans.", "publication": { "title": "Interactions between LHX3- and ISL1-family LIM-homeodomain transcription factors are conserved in Caenorhabditis elegans.", "author_list": "Bhati M, Llamosas E, Jacques DA, Jeffries CM, Dastmalchi S, Ripin N, Nicholas HR, Matthews JM", "journal": "Sci Rep", "doi": "10.1038/s41598-017-04587-8", "pmid": "28676648", "published_date": "2017 Jul 4" }, "status": "released", "submitted_date": null, "released_date": "2017-07-08" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDC22.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDC22.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC22_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC22_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDC22_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDC22_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDC22.sascif", "experiment": { "instrument": { "detector": { "type": "KAF 2084 x 2084 SCX CCD", "name": "Roper Scientific PI-SCX:4300", "resolution": 24.0 }, "name": "University of Sydney", "city": "Sydney", "country": "Australia", "beamline_name": "Anton Paar SAXSess", "beam_geometry": "Line collimation", "type_of_source": "X-ray in house", "point_source": false, "line_collimation": true, "sample_path_length": 1.0, "line_collimation_slitlength": 10.0, "line_collimation_integrationwidth": 10.0, "xray_energy": null, "beam_profile_ah": 2.8, "beam_profile_al": 1.3 }, "sample": { "molecule": [ { "long_name": "Homeobox protein CEH-14", "short_name": "CEH-14", "sequence": "GSNNEEAICSLCDKKIRDRFVSKVNGRCYHSSCLRCSTCKDELGATCFLREDSMYCRAHF \r\nYKKFGTKCSSCNEGIVPDHVVRKASNHVYHVECFQCFICKRSLETGEEFYLIADDARLVC \r\nKDDYEQARDGGSGGHMGSGG", "organism": "Caenorhabditis elegans", "uniprot_code": "P20271", "uniprot_range_first": 42, "uniprot_range_last": 168, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MLGHNILTLGECDELDNHIVMCSTGLLSPQEDFSNVNAGHPNNEEAICSLCDKKIRDRFV\nSKVNGRCYHSSCLRCSTCKDELGATCFLREDSMYCRAHFYKKFGTKCSSCNEGIVPDHVV\nRKASNHVYHVECFQCFICKRSLETGEEFYLIADDARLVCKDDYEQARDKHCNELEGDGSN\nKRPRTTISAKSLETLKQAYQTSSKPARHVREQLASETGLDMRVVQVWFQNRRAKEKRLKK\nDAGRRWKSSNRAESDSNSPIESINGQSPNYLYLDHPMDDGNESNYLFHSREQTPDKYYRN\nETPSTDPPPMHMTTPSVLTTNFSTPLSLSTNVYNLPPPESQLIPHMTPQYI", "mw": 15.693, "total_mw": 15.693, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null }, { "long_name": "CeLIM-7", "short_name": "CeLIM-7", "sequence": "GIGPLMVQPATPHIDNTLGGPIDIQHFAQWEF", "organism": "Caenorhabditis elegans", "uniprot_code": "G5EC36", "uniprot_range_first": 347, "uniprot_range_last": 376, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MNICMRNGYEQFSLTSPGTSDLEIGGSFWKDEPDTKYLCLDSPVEQRQHQPPMAVCAGCR\nLEISDRYFLRVNPNLEFHAQCLKCVQCSRPLDENQTAFVKNGQTYCRDDYRRLFTTRCSR\nCHGDFDKTDLVMRAGPQNVFHLNCFACVACEKRLQTGEEFQIKNNSLYCRSDCRGLDNPD\nTSASVPDYSKLNNNNNNDNNNSSSNFDEDEWDEERSTLTSLDNNTSSPLGSPKSDGVRTP\nLFGHHNSGSGGSTSSCGKKKKDKQATRVRTVLNENQLKILRDCYSINSRPDATLKERLVE\nMTGLSARVIRVWFQNKRCKDKKRQIQITENRLNSEREEVLNRVRVNGIGPLMVQPATPHI\nDNTLGGPIDIQHFAQWNGTPPPPPPQYGNPMMFNSPSTFDVSVILAPVAPNVTSPSEALG\nPLGASVFPHFSPQHAPFTATSHDISSPAPCGE", "mw": 3.501, "total_mw": 3.501, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "50 mM Tris, 100 mM NaCl, 5 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "EMBL-Hamburg", "address": "Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany", "full_name": "European Molecular Biology Laboratory (EMBL) - Hamburg outstation", "webpage": "http://www.embl-hamburg.de/index.php" } ], "contributor_name": "Cy M", "contributor_surname": "Jeffries", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2009-04-07", "storage_temperature": null, "cell_temperature": 10.0, "exposure_time": 900.0, "number_of_frames": 4, "wavelength": 0.1542, "sample_detector_distance": 0.309, "concentration_min": null, "concentration_max": 5.2, "sample_volume": null, "flow_rate": null, "s_min": 0.067, "s_max": 3.311, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit1_model1.pdb", "model_mw": 17.376, "bead_radius": 2.25, "log": null, "symmetry": "", "comment": "", "user": 9 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit1_model2_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit1_model2.pdb", "model_mw": 17.473, "bead_radius": 2.25, "log": null, "symmetry": "", "comment": "", "user": 9 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC22_fit1_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.288, "p_value": 0.1902, "fit_residual_plot": "SASDC22_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC22_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_hdm80LL.log", "software_version": "", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit2_model1_img.png", "software": "GASBOR", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit2_model1.pdb", "model_mw": null, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 9 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC22_fit2_fit_img.png", "software": "GASBOR", "chi_square_value": 0.29, "p_value": 0.0257, "fit_residual_plot": "SASDC22_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC22_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/Ceh5.log", "software_version": "", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDC22_fit3_model1_img.png", "software": "SwissModel", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDC22_fit3_model1.pdb", "model_mw": 18.77, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "", "user": 9 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDC22_fit3_fit_img.png", "software": "CRYSOL", "chi_square_value": 0.3, "p_value": 0.192, "fit_residual_plot": "SASDC22_fit3_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDC22_fit3.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/model_ceh14_lim7r_Znr00.log", "software_version": "", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "GNOM5 (r8972)", "i0_calibration_standard": null, "description": "The SAXS data displayed for this entry includes the beam-geometry corrected scattering profile (desmeared data, top, and homology model fit) as well as the fit of the ab initio models to the smeared SAXS data (i.e., smeared model-data fits). The original smeared data, prepared experimental beam profile and all individual DAMMIF and Gasbor models are included in the full entry zip archive.", "experiment_description": "SAXS data from solutions of the tandem LIM domains of the neuronal transcription factor homeobox protein CEH-14 fused to the LIM interaction domain of ceLIM-7 in 50 mM Tris, 100 mM NaCl, 5 mM TCEP, pH 8 were collected on an Anton Paar SAXSess 10 mm line collimated instrument (The University of Sydney, Australia) using a CCD Roper Scientific KAF 2084 x 2084 SCX CCD camera at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.1542 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). One solute concentration of 5.50 mg/ml was measured at 10°C. Four successive 900 second frames were collected. The data were normalized to the intensity of the transmitted beam and underwent 10 mm horizontal-width integration; the scattering of the solvent-blank was subtracted to produce the smeared scattering profile of the protein in solution.", "tags": [], "intensity_unit": null, "experimental_mw": 17.0, "experimental_mw_error": null, "guinier_i0_mw": 16.7, "guinier_i0_mw_error": 0.9, "porod_mw": 16.0, "porod_mw_error": null, "pddf_i0": 0.0833, "pddf_i0_error": 0.002, "guinier_i0": 0.083, "guinier_i0_error": 0.0002, "pddf_rg": 2.51, "pddf_rg_error": 0.09, "guinier_rg": 2.4, "guinier_rg_error": 0.03, "pddf_dmax": 8.9, "pddf_dmax_error": null, "porod_volume": 25.6, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 1, "guinier_point_last": 61, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDC22_datloglog_img.png", "symmetry": null, "last_modified": "2020-01-10T16:55:24.317339+01:00", "bragg_peak": [] }