{ "code": "SASDBY9", "status": "Published", "type_of_curve": "Single concentration", "angular_unit": "1/A", "project": { "title": "Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.", "publication": { "title": "Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex.", "author_list": "Upla P, Kim SJ, Sampathkumar P, Dutta K, Cahill SM, Chemmama IE, Williams R, Bonanno JB, Rice WJ, Stokes DL, Cowburn D, Almo SC, Sali A, Rout MP, Fernandez-Martinez J", "journal": "Structure", "doi": "10.1016/j.str.2017.01.006", "pmid": "28162953", "published_date": "2017 Mar 7" }, "status": "released", "submitted_date": "2017-01-23", "released_date": "2017-02-16" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDBY9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBY9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBY9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBY9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBY9.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Rayonix MX225-HE", "resolution": null }, "name": "Stanford Synchrotron Radiation Lightsource (SSRL)", "city": "Menlo Park, CA", "country": "USA", "beamline_name": "BL4-2", "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": "Nucleoporin POM152", "short_name": null, "sequence": "GKSNVLVTMPVAPTMEVKSFPILDQCVGQVGLNFELSFTGAPPYYYNTKIYKLENGERKLYDAKRYTSEGTRNRFSYSPPKEGNYEIVFDTVSNKLFTEPIKLEPVKEYTFKTSMRVKPSASLKLHHDLKLCLGDHSSVPVALKGQGPFTLTYDIIETFSSKRKTFEIKEIKTNEYVIKTPVFTTGGDYILSLVSIKDSTGCVVGLSQPDAKIQVRRDEGHHHHHH", "organism": "Saccharomyces cerevisiae", "uniprot_code": "P39685", "uniprot_range_first": null, "uniprot_range_last": null, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MEHRYNVFNDTPRGNHWMGSSVSGSPRPSYSSRPNVNTTRRFQYSDDEPAEKIRPLRSRS\nFKSTESNISDEKSRISERDSKDRYINGDKKVDIYSLPLISTDVLEISKQRTFAVILFLII\nQCYKIYDLVILKSGLPLSGLLFKNYRFNFISKYFIIDSFFLYVLPSFNIPRLTFKPWVVY\nLQILAMLLLNIFISSDHEFVLISLIMTTWRKLYTKELSVTGSAINHHRIFDSSAHFKGAL\nTIKILPENTAMFNPLHESYCLPMDTNLFKINSIDVPIRINSTEEIEYIELEYRDLYTNSV\nELRSLSKKDFKIIDNPKSFLKKDQSVLKSHSNDFEEGSTIRYLAVTLQDIGFYQIKKIVD\nSKKLNLKIHQSHLVVPYCPIASITGTGSNDRCIGDSDNVSFEIQGVPPMKLAYSKIVNGQ\nTFSYVDSSLQPEYFESPLQSSKSKQSFTQGELNDLKWGRNQPVNINLDSSITQDGKFAYK\nIDKITDGLGNVVDFTSLPEELKKRYDLSYNFNVHEVPRAALEERFDPKSPTKRSIAIVFE\nEIKNWISDIPYVISLSYTDAQDKSKKIMNVTTDSLTKVLQADLPGSYNLEYIESKFCPGE\nIVGKSNVLVTMPVAPTMEVKSFPILDQCVGQVGLNFELSFTGAPPYYYNTKIYKLENGER\nKLYDAKRYTSEGTRNRFSYSPPKEGNYEIVFDTVSNKLFTEPIKLEPVKEYTFKTSMRVK\nPSASLKLHHDLKLCLGDHSSVPVALKGQGPFTLTYDIIETFSSKRKTFEIKEIKTNEYVI\nKTPVFTTGGDYILSLVSIKDSTGCVVGLSQPDAKIQVRRDIPSAAFNFFEPIKEAKIKHG\nSVTEIPLKLSGEGPFTVKFKHMDYDGNIVKEFENKFQNSYKPALKVSKEGLYQLVDIRDS\nSCQGNVIYRNSLYKVSFLEKPKFAIQDNHHITKVTENLFSKEEVCQGMEGTVDLALFGSP\nPFILEYDLMAPNGHISTKKIQVATKYASLKLPNQIPGEYITTIKAIFDGNYGESDIHFRE\nHQSELIIKQTVHPIPDVAFADGGKTLRACAANVDQISFLEPINLKFLQGESPFSITFSVY\nHESTSRTDQYTIDNIDSENFSFEKLYEGMKLGNHAITIDSVVDANGCVNSLISGPRNQIL\nVSITDAPKIHILDPSTEYCVGDYVAYQLNGVAPFMIKYEFNGIPLKSKERSSQFVRLASE\nPGIISITSLQDSSSQCIVDFTNPKLKSEFDDLSLNIHPIPSVTVSQGNYVTEDIREGDQA\nEVIFSFEGTPPFSLTYVRTEETDGKHGKRRSQVVETHKVTDIYSHEYKVITSLQGTYEAI\nEITDAYCFAKNDLFFNN", "mw": 25.552, "total_mw": 25.552, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "10mM HEPES, 150mM NaCl, 10%(v/v) glycerol, 5mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.5, "deuteration": null }, "purity_method": null, "name": "Immunoglobulin domains 3,4 of Nucleoporin Pom152 (Pom152 Ig-3,4: amino acids 603-820)", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": "UCSF", "address": "San Francisco, CA, USA", "full_name": "University of California, San Francisco (UCSF)", "webpage": "https://www.ucsf.edu/" } ], "contributor_name": "Seung Joong", "contributor_surname": "Kim", "orcid": null } ], "concentration_method": null, "concentration_unit": null, "date": "2015-04-12", "storage_temperature": 15.0, "cell_temperature": 15.0, "exposure_time": 1.0, "number_of_frames": 20, "wavelength": 0.098, "sample_detector_distance": 1.7, "concentration_min": 0.5, "concentration_max": 11.9, "sample_volume": null, "flow_rate": null, "s_min": 0.096, "s_max": 3.616, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBY9_fit1_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBY9_fit1_model1.pdb", "model_mw": 22.245, "bead_radius": 2.25, "log": null, "symmetry": "", "comment": "", "user": 197 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBY9_fit1_fit_img.png", "software": "DAMMIN", "chi_square_value": 2.017, "p_value": 3e-06, "fit_residual_plot": "SASDBY9_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBY9_fit1.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/27005_25.log", "software_version": "5.3", "description": null } ], "estimated_volume_method": null, "pddf_software": "ATSAS GNOM", "pddf_software_version": "gnom 4.5a", "i0_calibration_standard": null, "description": "Guinier Rg and I(0) were calculated using AutoRg. The experimental MW was estimated using SAXSMOW.", "experiment_description": "Synchrotron SAXS data from solutions of Immunoglobulin domains 3,4 of Nucleoporin Pom152 (Pom152 Ig-3,4: amino acids 603-820) in 10mM HEPES, 150mM NaCl, 10%(v/v) glycerol, 5mM DTT, pH 7.5 were collected on the BL4-2 beam line at the Stanford Synchrotron Radiation Lightsource (SSRL) (Stanford, CA, USA) using a Rayonix MX225-HE detector at a sample-detector distance of 1.7 m and at a wavelength of λ = 0.098 nm (I(s) vs s, where = 4πsinθ/λ and 2θ is the scattering angle). Solute concentrations ranging between 0.5 and 11.9 mg/ml were measured at 15°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 and the different curves were scaled for protein concentration.", "tags": [], "intensity_unit": null, "experimental_mw": 25.9, "experimental_mw_error": null, "guinier_i0_mw": 25.2, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 1550.0, "pddf_i0_error": 1.71, "guinier_i0": 1553.37, "guinier_i0_error": 2.97, "pddf_rg": 2.976, "pddf_rg_error": 0.005, "guinier_rg": 2.95, "guinier_rg_error": 0.11, "pddf_dmax": 10.45, "pddf_dmax_error": null, "porod_volume": 27.97, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 3, "guinier_point_last": 23, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBY9_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }