{ "code": "SASDEA8", "status": "Published", "type_of_curve": "Merged", "angular_unit": "1/A", "project": { "title": "Full length of DnaG primase from Bacillus subtilis", "publication": null, "status": "released", "submitted_date": "2018-11-21", "released_date": "2021-09-20" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEA8.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEA8.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEA8_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEA8_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEA8_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEA8_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEA8.sascif", "experiment": { "instrument": { "detector": { "type": "Dectris", "name": "Pilatus 1M", "resolution": 172.0 }, "name": "Shanghai Synchrotron Radiation Facility (SSRF)", "city": "Shanghai", "country": "China", "beamline_name": "BL19U2", "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": "DNA primase", "short_name": null, "sequence": "MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFH\r\nCFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARPESSGEQKMAE\r\nAHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGF\r\nSEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPET\r\nPLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVISAVSSDVKESIATMGTSLTDDHVKI\r\nLRRNVEEIILCYDSDKAGYEATLKASELLQKKGCKVRVAMIPDGLDPDDYIKKFGGEKFK\r\nNDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVKQLASE\r\nFSLSQESLTEQLSVFSKQNKPADNSGETKTRRAHLTTKARQKRLRPAYENAERLLLAHML\r\nRDRSVIKKVIDRVGFQFNIDEHRALAAYLYAFYEEGAELTPQHLMARVTDDHISQLLSDI\r\nLMLQVNQELSEAELSDYVKKVLNQRNWSMIKEKEAERAEAERQKDFLRAASLAQEIVTLN\r\nRSLK", "organism": "Bacillus subtilis", "uniprot_code": "P05096", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MGNRIPDEIVDQVQKSADIVEVIGDYVQLKKQGRNYFGLCPFHGESTPSFSVSPDKQIFH\nCFGCGAGGNVFSFLRQMEGYSFAESVSHLADKYQIDFPDDITVHSGARPESSGEQKMAEA\nHELLKKFYHHLLINTKEGQEALDYLLSRGFTKELINEFQIGYALDSWDFITKFLVKRGFS\nEAQMEKAGLLIRREDGSGYFDRFRNRVMFPIHDHHGAVVAFSGRALGSQQPKYMNSPETP\nLFHKSKLLYNFYKARLHIRKQERAVLFEGFADVISAVSSDVKESIATMGTSLTDDHVKIL\nRRNVEEIILCYDSDKAGYEATLKASELLQKKGCKVRVAMIPDGLDPDDYIKKFGGEKFKN\nDIIDASVTVMAFKMQYFRKGKNLSDEGDRLAYIKDVLKEISTLSGSLEQEVYVKQLASEF\nSLSQESLTEQLSVFSKQNKPADNSGETKTRRAHLTTKARQKRLRPAYENAERLLLAHMLR\nDRSVIKKVIDRVGFQFNIDEHRALAAYLYAFYEEGAELTPQHLMARVTDDHISQLLSDIL\nMLQVNQELSEAELSDYVKKVLNQRNWSMIKEKEAERAEAERQKDFLRAASLAQEIVTLNR\nSLK", "mw": 68.735, "total_mw": 68.735, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "25 mM Tris-HCl,100 mM NaCl", "concentration_unit": null, "comment": "25 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM DTT", "additive": null, "concentration": null, "pka": null, "ph": 8.0, "deuteration": null }, "purity_method": null, "name": "Full length of DnaG (DNA Primase) from Bacillus subtilis", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Chengdu, China", "full_name": "Chengdu Institute of Biology, Chinese academy of Sciences", "webpage": "http://english.cib.cas.cn/" } ], "contributor_name": "Zhongchuan", "contributor_surname": "Liu", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2018-10-01", "storage_temperature": 10.0, "cell_temperature": 10.0, "exposure_time": 1.0, "number_of_frames": 20, "wavelength": 0.154, "sample_detector_distance": 2.0, "concentration_min": 1.0, "concentration_max": 7.0, "sample_volume": null, "flow_rate": null, "s_min": 0.084, "s_max": 3.954, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEA8_fit1_model1_img.png", "software": "CORAL", "pdb_link": [], "model_title": null, "type_of_model": "mix", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEA8_fit1_model1.pdb", "model_mw": 68.46, "bead_radius": 1.9, "log": null, "symmetry": null, "comment": null, "user": 240 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEA8_fit1_fixed_fit_img.png", "software": "CORAL", "chi_square_value": 0.95, "p_value": 0.554373, "fit_residual_plot": "SASDEA8_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEA8_fit1.fit", "fit_log": null, "software_version": null, "description": "" }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEA8_fit2_model1_img.png", "software": "DAMMIF", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEA8_fit2_model1.pdb", "model_mw": 82.8, "bead_radius": 5.0, "log": null, "symmetry": null, "comment": null, "user": 240 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEA8_fit2_fixed_fit_img.png", "software": "DAMMIF", "chi_square_value": 1.176, "p_value": 0.050515, "fit_residual_plot": "SASDEA8_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEA8_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 full length of DnaG (DNA Primase) from Bacillus subtilis in 25 mM Tris-HCl,100 mM NaCl, pH 8 were collected on the NCPSS BL19U2 beam line at the Shanghai Synchrotron Radiation Facility (SSRF; Shanghai, China) using a Dectris Pilatus 1M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.154 nm in the momentum transfer range of 0.2 < s < 4 1/nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). Solute concentrations ranging between 1 and 7 mg/ml were measured at 10°C. 20 successive 1 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 concentration were merged with the highest concentration high angle data to yield the final composite scattering curve.", "tags": [], "intensity_unit": "arbitrary", "experimental_mw": 70.0, "experimental_mw_error": null, "guinier_i0_mw": 70.0, "guinier_i0_mw_error": 2.0, "porod_mw": 74.0, "porod_mw_error": null, "pddf_i0": 90.9, "pddf_i0_error": null, "guinier_i0": 89.22, "guinier_i0_error": 0.24, "pddf_rg": 3.94, "pddf_rg_error": null, "guinier_rg": 3.74, "guinier_rg_error": 0.1, "pddf_dmax": 14.5, "pddf_dmax_error": null, "porod_volume": 119.0, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 7, "guinier_point_last": 56, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEA8_datloglog_img.png", "symmetry": null, "last_modified": "2021-09-20T13:42:19.789088+02:00", "bragg_peak": [] }