{ "code": "SASDBV9", "status": "Published", "type_of_curve": "Merged", "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/SASDBV9.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDBV9.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBV9_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBV9_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDBV9_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDBV9_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDBV9.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": "RVKPSASLKLHHDLKLCLGDHSSVPVALKGQGPFTLTYDIIETFSSKRKTFEIKEIKTNEYVIKTPVFTTGGDYILSLVSIKDSTGCVVGLSQPDAKIQVRRDEGHHHHHH", "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": 12.386, "total_mw": 12.386, "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 domain 4 of Nucleoporin Pom152 (Pom152 Ig-4: amino acids 718-820)", "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": 0.151, "s_max": 3.616, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBV9_fit1_model1_img.png", "software": "MODELLER", "pdb_link": [ { "pdb_code": "5tvz", "ext_code": "5TVZ", "ext_type": "pdb", "difference_with_model": "derived" } ], "model_title": null, "type_of_model": "atomic", "software_version": "9.13", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBV9_fit1_model1.pdb", "model_mw": 12.39, "bead_radius": 1.9, "log": null, "symmetry": "", "comment": "A histag was modelled using MODELLER", "user": 197 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBV9_fit1_fit_img.png", "software": "FoXS", "chi_square_value": 1.13, "p_value": 0.011, "fit_residual_plot": null, "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBV9_fit1.fit", "fit_log": null, "software_version": "", "description": null }, { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDBV9_fit2_model1_img.png", "software": "DAMMIN", "pdb_link": [], "model_title": null, "type_of_model": "dummy", "software_version": "5.3", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDBV9_fit2_model1.pdb", "model_mw": 11.615, "bead_radius": 1.5, "log": "https://www.sasbdb.org/media/log_files/26993_1.log", "symmetry": "", "comment": "", "user": 197 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDBV9_fit2_fit_img.png", "software": "DAMMIN", "chi_square_value": 1.103, "p_value": 0.005555, "fit_residual_plot": "SASDBV9_fit2_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDBV9_fit2.fir", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/26993_1.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 domain 4 of Nucleoporin Pom152 (Pom152 Ig-4: amino acids 718-820) 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 s = 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. 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": null, "experimental_mw": 12.6, "experimental_mw_error": null, "guinier_i0_mw": 12.2, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 155.0, "pddf_i0_error": 0.2801, "guinier_i0": 154.07, "guinier_i0_error": 0.33, "pddf_rg": 1.824, "pddf_rg_error": 0.006, "guinier_rg": 1.77, "guinier_rg_error": 0.048, "pddf_dmax": 6.66, "pddf_dmax_error": null, "porod_volume": 17.94, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 17, "guinier_point_last": 58, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDBV9_datloglog_img.png", "symmetry": null, "last_modified": "2019-12-06T13:07:15.624532+01:00", "bragg_peak": [] }