{"code":"SASDEX9","status":"Published","type_of_curve":"SEC-SAS","angular_unit":"1/nm","project":{"title":" <scp>EFAMIX</scp>\n              , a tool to decompose inline chromatography <scp>SAXS</scp>\n              data from partially overlapping components","publication":{"title":" <scp>EFAMIX</scp>\n              , a tool to decompose inline chromatography <scp>SAXS</scp>\n              data from partially overlapping components","author_list":"Konarev P, Graewert M, Jeffries C, Fukuda M, Cheremnykh T, Volkov V, Svergun D","journal":"Protein Science","doi":"10.1002/pro.4237","pmid":null,"published_date":"2021 Nov 22"},"status":"released","submitted_date":"2021-01-17","released_date":"2021-11-24"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDEX9.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDEX9.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX9_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX9_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEX9_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEX9_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDEX9.sascif","experiment":{"instrument":{"detector":{"type":null,"name":"Pilatus 6M","resolution":null},"name":"PETRA III","city":"DESY; Hamburg","country":"Germany","beamline_name":"EMBL P12","beam_geometry":null,"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":"HpcH/HpaI aldolase","short_name":null,"sequence":"MHHHHHHNKVRTCWNEGRPALAGWLQLPGTLHAEALARLDYDAVVIDMQHSPIDFGQVAPMLIAIELGGAEPFVRTQV\r\nNDPSDIMKLLDAGAYGIIAPMVNTRAEAQTLASALHYSPRGLRSFGPRRPSLRYGSGYLAQASETVVGLAMIETREAL\r\nANIDEILSVDGIDGVFIGPTDLALDLGHAPLVDTEEAEVVSAIAHVRERAHAAGKRVGIFCGSGGFARVKLAEGFDFV\r\nTAAPDLAMLSAAARQVIADARAL","organism":"Rhizorhabdus wittichii RW1","uniprot_code":"A5VH82","uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"hexamer","molecular_type":"protein","uniprot_sequence":"MNKVRTCWNEGRPALAGWLQLPGTLHAEALARLDYDAVVIDMQHSPIDFGQVAPMLIAIE\r\nLGGAEPFVRTQVNDPSDIMKLLDAGAYGIIAPMVNTRAEAQTLASALHYSPRGLRSFGPR\r\nRPSLRYGSGYLAQASETVVGLAMIETREALANIDEILSVDGIDGVFIGPTDLALDLGHAP\r\nLVDTEEAEVVSAIAHVRERAHAAGKRVGIFCGSGGFARVKLAEGFDFVTAAPDLAMLSAA\r\nARQVIADARAL","mw":27.435,"total_mw":164.61,"number_molecules":6,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":"Construct contains a N-terminal polyhistidine tag (MHHHHHH)."}],"buffer":{"name":"20 mM HEPES,","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Class II pyruvate aldolase (HpcH/HpaI aldolase), wild-type hexamer in HEPES isolated using SEC-SAXS","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":"2018-11-23","storage_temperature":20.0,"cell_temperature":20.0,"exposure_time":1.0,"number_of_frames":51,"wavelength":0.124,"sample_detector_distance":3.0,"concentration_min":null,"concentration_max":8.0,"sample_volume":null,"flow_rate":null,"s_min":0.091,"s_max":7.253,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEX9_fit1_model1_img.png","software":"GASBOR","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDEX9_fit1_model1.pdb","model_mw":null,"bead_radius":1.9,"log":null,"symmetry":"P32","comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEX9_fit1_fixed_fit_img.png","software":"GASBOR","chi_square_value":1.07,"p_value":0.158445,"fit_residual_plot":"SASDEX9_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEX9_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/9.log","software_version":"2.31","description":""},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDEX9_fit2_model1_img.png","software":"PDB (Protein Data Bank)","pdb_link":[{"pdb_code":"6r62","ext_code":"6R62","ext_type":"pdb","difference_with_model":"identical"}],"model_title":null,"type_of_model":"atomic","software_version":"PDB","model_data":"https://www.sasbdb.org/media/pdb_file/SASDEX9_fit2_model1.pdb","model_mw":160.5,"bead_radius":1.9,"log":"https://www.sasbdb.org/media/log_files/6R62_hexamerr_noMg00.log","symmetry":null,"comment":null,"user":9}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEX9_fit2_fixed_fit_img.png","software":"CRYSOL","chi_square_value":1.094,"p_value":0.0121,"fit_residual_plot":"SASDEX9_fit2_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDEX9_fit2.fit","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":"The quoted experimental MW is that determined from MALLS.","experiment_description":"Synchrotron SAXS data from solutions of hydroxypyruvate aldolase in 20 mM HEPES, pH 7.5 were collected using size exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at PETRA III (Hamburg, Germany) equipped with a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). The SEC parameters were as follows: An 80 μl sample at 8 mg/ml was injected at room temperature onto a GE Healthcare Superdex 200 Increase 10/300 column at a flow rate of 0.4 mL/min. 51 successive 1 second frames were collected through the lagging region of the SEC-elution peak that corresponded to the molecular weight (MW) of the hexamer (as assessed using multi-angle laser light scattering/refractive index measurements; MALLS/RI). The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted and the data scaled and averaged to produce the final SAXS profile displayed in this entry. CHROMIXS was used to process the SEC-SAXS data and assess the MW and Rg through the SEC peak (Rg and MW estimates and unsubtracted individual SEC-SAXS data frames are included in the full entry zip archive).","tags":[],"intensity_unit":"arbitrary","experimental_mw":157.0,"experimental_mw_error":null,"guinier_i0_mw":null,"guinier_i0_mw_error":null,"porod_mw":146.0,"porod_mw_error":null,"pddf_i0":1324.0,"pddf_i0_error":null,"guinier_i0":1320.69,"guinier_i0_error":2.0,"pddf_rg":3.325,"pddf_rg_error":null,"guinier_rg":3.34,"guinier_rg_error":0.01,"pddf_dmax":9.35,"pddf_dmax_error":null,"porod_volume":233.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":19,"guinier_point_last":110,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDEX9_datloglog_img.png","symmetry":null,"last_modified":"2023-06-21T07:55:24.740692+02:00","bragg_peak":[]}