{ "code": "SASDEY6", "status": "Published", "type_of_curve": "SEC-SAS", "angular_unit": "1/nm", "project": { "title": "Structural Characterisation of the Arabidopsis thaliana APC4", "publication": null, "status": "released", "submitted_date": "2018-10-29", "released_date": "2020-12-12" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEY6.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEY6.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY6_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY6_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEY6_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEY6_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEY6.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "ESRF", "city": "Grenoble", "country": "France", "beamline_name": "BM29", "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": "Anaphase Promoting Complex/Cyclosome Subunit 4", "short_name": "Apc4", "sequence": ">APC4-strep\r\nMSEMASDEEENIIPFQLQFDKPIPFQIKIAEWNPEKDLLAMVTEDSKILLHRFNWQRLWTISPGKPVTSLCWRPDGKAIAVGLEDGTISLHDVENGKLLRNLKPHDVAVVCLNWEEDGQSNTDESGNFSVYEDRTSRFFPPAPRPPKMPGLVAGDSSFMDDGEDSLAELSNTSFRKFNILCTGDRDGNICFSIFGIFQIGKINIHELSLPVPHLDEHASCKLFNASIYKVALSKDLCRLVVMCTGELKDCDIKPREEKINVQDLPGLHCLAMDTSIFWKRKYELHQVAQQASNIEDLTEVIRASLSVMNKQWADAMKTFHEKFHSLSTLIIDNGLESSPQEEFLSLLGGARISPALNQFLVNSLGEVGVKRVLKSVCGTGKELQQVVLDHLQPAAEIIGFRIGELRGLSRWRARYQGIGLDEMLLNEATENTGLLLVQVQRFMMVLSSVVQQFSNFFNWLVRSIKYLMQEPNDQLLSYNSELLVVFLKFLYDQDPVKDLLELSEAGDDIEIDLKTIGRVKELLQFGGFSECDFLQRTLAKEFQHMESSFKMAFQMPFTTISRKISCMKLLPLCPLQLSTTQTPTTIPMSLSFYKNELSDDTPCQSGYTDYISFQVPDETFPEISNCIGIAKGYKQNSNNEKNGYTSLEAVLLSVPNGYTCVDLSLYKDKELVLLLNKTNTDSEGSGEACMMVVQTGDLAFISISGSSSLNQWELEDLKGSIVNLEMENEKVRKVPHSVIAPLAVSASRGVACVFAERRRALVYILEEDEDEEISDEKDYDIPTTENLYFQGSAWSHPQFEKGGGSGGGSGGGSWSHPQFEK", "organism": "Arabidopsis thaliana", "uniprot_code": "O65418", "uniprot_range_first": 1, "uniprot_range_last": 777, "oligomerization": "dimer", "molecular_type": "protein", "uniprot_sequence": "MSEMASDEEENIIPFQLQFDKPIPFQIKIAEWNPEKDLLAMVTEDSKILLHRFNWQRLWT\nISPGKPVTSLCWRPDGKAIAVGLEDGTISLHDVENGKLLRNLKPHDVAVVCLNWEEDGQS\nNTDESGNFSVYEDRTSRFFPPAPRPPKMPGLVAGDSSFMDDGEDSLAELSNTSFRKFNIL\nCTGDRDGNICFSIFGIFQIGKINIHELSLPVPHLDEHASCKLFNASIYKVALSKDLCRLV\nVMCTGELKDCDIKPREEKINVQDLPGLHCLAMDTSIFWKRKYELHQVAQQASNIEDLTEV\nIRASLSVMNKQWADAMKTFHEKFHSLSTLIIDNGLESSPQEEFLSLLGGARISPALNQFL\nVNSLGEVGVKRVLKSVCGTGKELQQVVLDHLQPAAEIIGFRIGELRGLSRWRARYQGIGL\nDEMLLNEATENTGLLLVQVQRFMMVLSSVVQQFSNFFNWLVRSIKYLMQEPNDQLLSYNS\nELLVVFLKFLYDQDPVKDLLELSEAGDDIEIDLKTIGRVKELLQFGGFSECDFLQRTLAK\nEFQHMESSFKMAFQMPFTTISRKISCMKLLPLCPLQLSTTQTPTTIPMSLSFYKNELSDD\nTPCQSGYTDYISFQVPDETFPEISNCIGIAKGYKQNSNNEKNGYTSLEAVLLSVPNGYTC\nVDLSLYKDKELVLLLNKTNTDSEGSGEACMMVVQTGDLAFISISGSSSLNQWELEDLKGS\nIVNLEMENEKVRKVPHSVIAPLAVSASRGVACVFAERRRALVYILEEDEDEEISDEK", "mw": 92.09, "total_mw": 184.18, "number_molecules": 2, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10 mM Tris 150 mM NaCl 1 mM TCEP", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Arabidopsis thaliana anaphase promoting complex/cyclosome subunit 4 (APC4-strep)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "VUB", "address": "Pleinlaan 2 1050 Brussel ", "full_name": "Vrije Universiteit Brussel", "webpage": "http://www.vub.ac.be/" } ], "contributor_name": "Steven", "contributor_surname": "De Gieter", "orcid": "" } ], "concentration_method": null, "concentration_unit": null, "date": "2017-03-06", "storage_temperature": 4.0, "cell_temperature": 20.0, "exposure_time": 1.0, "number_of_frames": 69, "wavelength": 0.099, "sample_detector_distance": 2.867, "concentration_min": 8.1, "concentration_max": 8.1, "sample_volume": null, "flow_rate": null, "s_min": 0.036, "s_max": 3.51, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEY6_fit1_model1_img.png", "software": "SREFLEX", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEY6_fit1_model1.pdb", "model_mw": 184.1, "bead_radius": null, "log": null, "symmetry": "P2", "comment": null, "user": 384 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEY6_fit1_fixed_fit_img.png", "software": "CRYSOL", "chi_square_value": 3.102, "p_value": 0.0, "fit_residual_plot": "SASDEY6_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEY6_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/rc0100.log", "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEY6_fit2_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEY6_fit2_model1.pdb", "model_mw": 160.835, "bead_radius": 3.9, "log": null, "symmetry": "P2", "comment": null, "user": 384 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEY6_fit2_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 0.788, "p_value": 0.000665, "fit_residual_plot": "SASDEY6_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEY6_fit2.fir", "fit_log": null, "software_version": null, "description": "" } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "5.0", "i0_calibration_standard": null, "description": null, "experiment_description": "Synchrotron SAXS data from solutions of anaphase promoting complex/cyclosome subunit 4 in 10 mM Tris ,150 mM NaCl, 1 mM TCEP, pH 8 were collected using size exclusion chromatography SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.099 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed using the following parameters: Column type: Shodex KW404-4F; Injection volume: 50 µl; Sample injection concentration: 8.1 mg/ml. 69 successive 1 second frames were collected through the elution peak (measured at 20°C). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the individual subtracted data sets were scaled and averaged to generate the scattering profile displayed in this entry.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 192.0, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": 162.0, "porod_mw_error": null, "pddf_i0": 50.1, "pddf_i0_error": null, "guinier_i0": 49.9, "guinier_i0_error": 0.042, "pddf_rg": 4.702, "pddf_rg_error": null, "guinier_rg": 4.64, "guinier_rg_error": 0.01, "pddf_dmax": 16.2, "pddf_dmax_error": null, "porod_volume": 259.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 19, "guinier_point_last": 53, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEY6_datloglog_img.png", "symmetry": null, "last_modified": "2020-12-12T16:01:14.893165+01:00", "bragg_peak": [] }