{"code":"SASDDZ8","status":"Published","type_of_curve":"Extrapolated to infinite dilution","angular_unit":"1/nm","project":{"title":"Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces.","publication":{"title":"Design of Hollow Protein Nanoparticles with Modifiable Interior and Exterior Surfaces.","author_list":"Kawakami N, Kondo H, Matsuzawa Y, Hayasaka K, Nasu E, Sasahara K, Arai R, Miyamoto K","journal":"Angew Chem Int Ed Engl","doi":"10.1002/anie.201805565","pmid":"30066354","published_date":"2018 Jul 31"},"status":"released","submitted_date":"2018-06-24","released_date":"2018-08-03"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDDZ8.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDDZ8.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ8_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ8_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDDZ8_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDDZ8_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDDZ8.sascif","experiment":{"instrument":{"detector":{"type":"Reverse-biased silicon diode array","name":"Pilatus3 1M","resolution":172.0},"name":"Photon Factory (PF), High Energy Accelerator Research Organization (KEK)","city":"Tsukuba","country":"Japan","beamline_name":"BL-6A","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":"Fusion protein of LSm and MyoX-coil","short_name":"TIP60 protomer","sequence":"MGSSHHHHHHSQDPKNIKIMRLVTGEDIIGNISESQGLITIKKAFVIIPMQATPGKPVQLVLSPWQPYTDDKEIVIDDSKVITITSPKDDIIKSYESHTRVLENKQVEEILRLEKEIEDLQRMKEQQELSLTEASLQKLQERRDQELRRLEEE","organism":"Artificial protein","uniprot_code":null,"uniprot_range_first":null,"uniprot_range_last":null,"oligomerization":"other","molecular_type":"protein","uniprot_sequence":null,"mw":17.766,"total_mw":1065.96,"number_molecules":60,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":8.0,"deuteration":null},"purity_method":null,"name":"Designed hollow protein nanoparticle TIP60 (Truncated Icosahedral Protein composed of 60-mer fusion proteins)","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":null,"address":"Japan","full_name":"Shinshu University","webpage":"https://www.shinshu-u.ac.jp"}],"contributor_name":"Ryoichi","contributor_surname":"Arai","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2017-11-11","storage_temperature":null,"cell_temperature":25.0,"exposure_time":5.0,"number_of_frames":30,"wavelength":0.15,"sample_detector_distance":2.023,"concentration_min":0.98,"concentration_max":4.97,"sample_volume":null,"flow_rate":null,"s_min":0.057,"s_max":2.603,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDDZ8_fit1_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/SASDDZ8_fit1_model1.pdb","model_mw":2037.4,"bead_radius":8.25,"log":null,"symmetry":null,"comment":null,"user":303},{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDDZ8_fit1_model2_img.png","software":"DAMFILT","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":null,"model_data":"https://www.sasbdb.org/media/pdb_file/SASDDZ8_fit1_model2.pdb","model_mw":1853.051,"bead_radius":8.25,"log":null,"symmetry":null,"comment":null,"user":303}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/refine_ws44bWi_fit_img.png","software":"DAMMIN","chi_square_value":2.976,"p_value":1e-06,"fit_residual_plot":"refine_ws44bWi_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDDZ8_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/refine_pVhvL37.log","software_version":null,"description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"5.0","i0_calibration_standard":null,"description":"The ab initio dummy atom bead models displayed in this entry are: Top - a refined DAMMIN model and corresponding fit generated from 20 individual model spatial alignments; Bottom - the bead-occupancy and volume-corrected (averaged) spatial representation of TIP60 (DAMFILT) obtained from 20 individual model spatial alignments.","experiment_description":"Synchrotron SAXS data from solutions of a designed hollow protein nanoparticle, TIP60, in 25 mM HEPES, 100 mM NaCl, 1 mM EDTA, 5% glycerol, pH 8 were collected on the BL-6A beam line at the Photon Factory (PF), High Energy Acceleration Reserch Organization (KEK) storage ring (Tsukuba, Japan) using a PILATUS3 1M detector at a sample-detector distance of 2.0 m and at a wavelength of λ = 0.15 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1.0 and 5.0 mg/ml were measured at 25°C. 30 successive 5 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted. The low angle data collected at lower concentrations were extrapolated to infinite dilution and merged with the higher concentration data to yield the final composite scattering curve.","tags":[],"intensity_unit":"1/cm","experimental_mw":1063.0,"experimental_mw_error":null,"guinier_i0_mw":1063.0,"guinier_i0_mw_error":null,"porod_mw":null,"porod_mw_error":null,"pddf_i0":0.6241,"pddf_i0_error":null,"guinier_i0":0.643,"guinier_i0_error":0.001,"pddf_rg":8.952,"pddf_rg_error":null,"guinier_rg":9.39,"guinier_rg_error":0.06,"pddf_dmax":23.0,"pddf_dmax_error":null,"porod_volume":null,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":4,"guinier_point_last":23,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDDZ8_datloglog_img.png","symmetry":null,"last_modified":"2021-08-18T17:32:55.174589+02:00","bragg_peak":[]}