{"code":"SASDCK2","status":"Published","type_of_curve":"Other","angular_unit":"1/A","project":{"title":"2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.","publication":{"title":"2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.","author_list":"Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE","journal":"Acta Crystallogr D Struct Biol","doi":"10.1107/S2059798317011597","pmid":"28876235","published_date":"2017 Sep 1"},"status":"released","submitted_date":"2017-05-06","released_date":"2017-08-22"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDCK2.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDCK2.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCK2_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCK2_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDCK2.sascif","experiment":{"instrument":{"detector":{"type":"Dectris","name":"Pilatus 1M","resolution":172.0},"name":"Australian  Synchrotron","city":"Melbourne","country":"Australia","beamline_name":"SAXS/WAXS","beam_geometry":"Point","type_of_source":"X-ray synchrotron","point_source":true,"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":"Xylose isomerase","short_name":"Glucose Isomerase","sequence":"MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIP\r\nFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTI\r\nRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAI\r\nEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK\r\nLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW\r\nASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEF\r\nDVDAAAARGMAFERLDQLAMDHLLGARG","organism":"Streptomyces rubiginosus","uniprot_code":"P24300","uniprot_range_first":1,"uniprot_range_last":388,"oligomerization":"tetramer","molecular_type":"protein","uniprot_sequence":"MNYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIP\nFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTI\nRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAI\nEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGK\nLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVW\nASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEF\nDVDAAAARGMAFERLDQLAMDHLLGARG","mw":43.227,"total_mw":172.908,"number_molecules":4,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":""}],"buffer":{"name":"25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3","concentration_unit":null,"comment":"2 mM TCEP and 0.1% (.01538 M) NaN3 used  for radiation protection","additive":null,"concentration":null,"pka":null,"ph":7.5,"deuteration":null},"purity_method":null,"name":"Glucose Isomerase - Streptomyces rubiginosus","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Sydney, New South Wales 2006, Australia","full_name":"School of Molecular Bioscience, University of Sydney.","webpage":""}],"contributor_name":"Jill","contributor_surname":"Trewhella","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2017-03-09","storage_temperature":null,"cell_temperature":22.0,"exposure_time":1.0,"number_of_frames":24,"wavelength":0.10332,"sample_detector_distance":2.683,"concentration_min":0.06,"concentration_max":0.34,"sample_volume":null,"flow_rate":null,"s_min":0.066,"s_max":3.104,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDCK2_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"on-line","model_data":"https://www.sasbdb.org/media/pdb_file/SASDCK2_fit1_model1.pdb","model_mw":120.74,"bead_radius":2.4,"log":"https://www.sasbdb.org/media/log_files/GIstderr.log","symmetry":"P1","comment":"job submitted ATSAS on-line April 9, 2017","user":138}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK2_fit1_fixed_fit_img.png","software":"DAMMIN","chi_square_value":0.951,"p_value":0.035,"fit_residual_plot":"SASDCK2_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDCK2_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/GIstderr.log","software_version":"on-line","description":null},{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/GI_tet_img.png","software":"FoXS","pdb_link":[{"pdb_code":"1oad","ext_code":"1OAD","ext_type":"pdb","difference_with_model":"derived"}],"model_title":null,"type_of_model":"atomic","software_version":"on-line","model_data":"https://www.sasbdb.org/media/pdb_file/SASDCK2_fit2_model1.pdb","model_mw":173.7,"bead_radius":1.9,"log":null,"symmetry":"","comment":"GI tetramer generated from PDB:1OAD using symmetry transforms in pymol","user":138}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCK2_fit2_fitfoxs_img.png","software":"FoXS","chi_square_value":1.02,"p_value":0.045511,"fit_residual_plot":"SASDCK2_fit2_fitfoxsresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDCK2_fit2.dat","fit_log":null,"software_version":"on-line","description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"GNOM","i0_calibration_standard":null,"description":null,"experiment_description":"Synchrotron SAXS data from solutions of glucoes isomerase in 25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3, pH 7.5 were collected on the SAXS/WAXS beam line at Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Scattering data are on an absolute scale (cm-1) set by reference to the scattering from pure H2O. I(0) values must be corrected for the shear flow sample cell by a 2.05 multiplicative factor. Data were acquired in SEC-SAXS mode, summed from 21 measurement frames where Rg was flat and at a maximum. The average concentration over the frames was 0.18 mg/mL, spanning values from 0.06 - 0.34 mg/mL. Sample concentrations were measured by A280 (extinction coefficient for 1 mg/mL, 10 mm pathlength; E0.1% = 1.079), corrected for the 3.1 mm path-length of the UV measurement cell. MULCh was used to calculate the partial specific volume (0.732 mL/g) and X-ray contrast (Δρ = 2.833e10 cm-2). The protein is a tetramer in the solution conditions measured.","tags":["benchmark"],"intensity_unit":"1/cm","experimental_mw":172.234,"experimental_mw_error":null,"guinier_i0_mw":183.254,"guinier_i0_mw_error":null,"porod_mw":152.667,"porod_mw_error":null,"pddf_i0":0.03739,"pddf_i0_error":3.9e-05,"guinier_i0":0.037,"guinier_i0_error":4.4e-05,"pddf_rg":3.265,"pddf_rg_error":0.004,"guinier_rg":3.287,"guinier_rg_error":0.013,"pddf_dmax":9.22,"pddf_dmax_error":null,"porod_volume":229.0,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":1,"guinier_point_last":43,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDCK2_datloglog_img.png","symmetry":null,"last_modified":"2024-03-08T11:32:18.321280+01:00","bragg_peak":[]}