{ "code": "SASDEV2", "status": "Published", "type_of_curve": "Extrapolated to infinite dilution", "angular_unit": "1/nm", "project": { "title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.", "publication": { "title": "Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.", "author_list": "Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA", "journal": "Proc Natl Acad Sci U S A", "doi": "10.1073/pnas.1704692114", "pmid": "28716919", "published_date": "2017 Aug 1" }, "status": "released", "submitted_date": "2018-08-16", "released_date": "2018-08-18" }, "pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDEV2.out", "intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDEV2.dat", "intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEV2_dat_img.png", "intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEV2_kratky_img.png", "pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDEV2_pofr_img.png", "intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDEV2_guinier_img.png", "sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDEV2.sascif", "experiment": { "instrument": { "detector": { "type": null, "name": "Pilatus 2M", "resolution": null }, "name": "PETRA III", "city": "DESY; Hamburg", "country": "Germany", "beamline_name": "EMBL P12", "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": "Nuclear pore complex protein Nup153", "short_name": "NUS", "sequence": "> U=p-acetylphenylalanine. \r\nGCPSASPAFGANQTPTFGQSQGASQPNPPGFGSISSSTALFPTGSQPAPPTFGTVSSSSQPPVFGQQPSQSAFGSGTTPNUA", "organism": "Homo sapiens", "uniprot_code": "P49790", "uniprot_range_first": 1313, "uniprot_range_last": 1390, "oligomerization": "monomer", "molecular_type": "protein", "uniprot_sequence": "MASGAGGVGGGGGGKIRTRRCHQGPIKPYQQGRQQHQGILSRVTESVKNIVPGWLQRYFN\nKNEDVCSCSTDTSEVPRWPENKEDHLVYADEESSNITDGRITPEPAVSNTEEPSTTSTAS\nNYPDVLTRPSLHRSHLNFSMLESPALHCQPSTSSAFPIGSSGFSLVKEIKDSTSQHDDDN\nISTTSGFSSRASDKDITVSKNTSLPPLWSPEAERSHSLSQHTATSSKKPAFNLSAFGTLS\nPSLGNSSILKTSQLGDSPFYPGKTTYGGAAAAVRQSKLRNTPYQAPVRRQMKAKQLSAQS\nYGVTSSTARRILQSLEKMSSPLADAKRIPSIVSSPLNSPLDRSGIDITDFQAKREKVDSQ\nYPPVQRLMTPKPVSIATNRSVYFKPSLTPSGEFRKTNQRIDNKCSTGYEKNMTPGQNREQ\nRESGFSYPNFSLPAANGLSSGVGGGGGKMRRERTRFVASKPLEEEEMEVPVLPKISLPIT\nSSSLPTFNFSSPEITTSSPSPINSSQALTNKVQMTSPSSTGSPMFKFSSPIVKSTEANVL\nPPSSIGFTFSVPVAKTAELSGSSSTLEPIISSSAHHVTTVNSTNCKKTPPEDCEGPFRPA\nEILKEGSVLDILKSPGFASPKIDSVAAQPTATSPVVYTRPAISSFSSSGIGFGESLKAGS\nSWQCDTCLLQNKVTDNKCIACQAAKLSPRDTAKQTGIETPNKSGKTTLSASGTGFGDKFK\nPVIGTWDCDTCLVQNKPEAIKCVACETPKPGTCVKRALTLTVVSESAETMTASSSSCTVT\nTGTLGFGDKFKRPIGSWECSVCCVSNNAEDNKCVSCMSEKPGSSVPASSSSTVPVSLPSG\nGSLGLEKFKKPEGSWDCELCLVQNKADSTKCLACESAKPGTKSGFKGFDTSSSSSNSAAS\nSSFKFGVSSSSSGPSQTLTSTGNFKFGDQGGFKIGVSSDSGSINPMSEGFKFSKPIGDFK\nFGVSSESKPEEVKKDSKNDNFKFGLSSGLSNPVSLTPFQFGVSNLGQEEKKEELPKSSSA\nGFSFGTGVINSTPAPANTIVTSENKSSFNLGTIETKSASVAPFTCKTSEAKKEEMPATKG\nGFSFGNVEPASLPSASVFVLGRTEEKQQEPVTSTSLVFGKKADNEEPKCQPVFSFGNSEQ\nTKDENSSKSTFSFSMTKPSEKESEQPAKATFAFGAQTSTTADQGAAKPVFSFLNNSSSSS\nSTPATSAGGGIFGSSTSSSNPPVATFVFGQSSNPVSSSAFGNTAESSTSQSLLFSQDSKL\nATTSSTGTAVTPFVFGPGASSNNTTTSGFGFGATTTSSSAGSSFVFGTGPSAPSASPAFG\nANQTPTFGQSQGASQPNPPGFGSISSSTALFPTGSQPAPPTFGTVSSSSQPPVFGQQPSQ\nSAFGSGTTPNSSSAFQFGSSTTNFNFTNNSPSGVFTFGANSSTPAASAQPSGSGGFPFNQ\nSPAAFTVGSNGKNVFSSSGTSFSGRKIKTAVRRRK", "mw": 7.979, "total_mw": 7.979, "number_molecules": 1, "complex_state": false, "deuteration": null, "molecule_source": "biological", "molecule_description": null } ], "buffer": { "name": "PBS, 10 mM DTT", "concentration_unit": null, "comment": null, "additive": null, "concentration": null, "pka": null, "ph": 7.4, "deuteration": null }, "purity_method": null, "name": "Unlabeled nuclear pore complex protein Nup153 (NUS) without denaturant", "ext_coefficient": null, "contrast": null, "specific_vol": null, "dry_vol": null, "absorbption": null, "deuteration": null, "mixture": null }, "contributor": [ { "affiliation": [ { "short_name": null, "address": "Prague, Czech Republic", "full_name": "Institute of Biotechnology CAS v.v.i.", "webpage": "http://www.ibt.cas.cz/" } ], "contributor_name": "Gustavo", "contributor_surname": "Fuertes Vives", "orcid": "https://orcid.org/0000-0002-8564-8644" } ], "concentration_method": null, "concentration_unit": null, "date": "2013-11-08", "storage_temperature": null, "cell_temperature": 23.0, "exposure_time": 0.05, "number_of_frames": 20, "wavelength": 0.1, "sample_detector_distance": 3.0, "concentration_min": 1.0, "concentration_max": 10.0, "sample_volume": null, "flow_rate": null, "s_min": 0.029, "s_max": 4.488, "total_exposure_time": null, "seccolumn": null }, "fits": [ { "models": [ { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV2_fit1_model1_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": null, "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV2_fit1_model1.pdb", "model_mw": 7.987, "bead_radius": null, "log": null, "symmetry": null, "comment": "p-acetylphenylalanine was replaced with a cysteine.", "user": 359 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV2_fit1_model2_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "CAMPARI", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV2_fit1_model2.pdb", "model_mw": 7.987, "bead_radius": null, "log": null, "symmetry": null, "comment": "p-acetylphenylalanine was replaced with a cysteine.", "user": 359 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV2_fit1_model3_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "CAMPARI", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV2_fit1_model3.pdb", "model_mw": 7.987, "bead_radius": null, "log": null, "symmetry": null, "comment": "p-acetylphenylalanine was replaced with a cysteine.", "user": 359 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV2_fit1_model4_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "CAMPARI", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV2_fit1_model4.pdb", "model_mw": 7.987, "bead_radius": null, "log": null, "symmetry": null, "comment": "p-acetylphenylalanine was replaced with a cysteine.", "user": 359 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV2_fit1_model5_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "CAMPARI", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV2_fit1_model5.pdb", "model_mw": 7.987, "bead_radius": null, "log": null, "symmetry": null, "comment": "p-acetylphenylalanine was replaced with a cysteine.", "user": 359 }, { "model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDEV2_fit1_model6_img.png", "software": "Other", "pdb_link": [], "model_title": null, "type_of_model": "atomic", "software_version": "CAMPARI", "model_data": "https://www.sasbdb.org/media/pdb_file/SASDEV2_fit1_model6.pdb", "model_mw": 7.987, "bead_radius": null, "log": null, "symmetry": null, "comment": "p-acetylphenylalanine was replaced with a cysteine.", "user": 359 } ], "fit_unit": "1/A", "fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDEV2_fit1_fixed_fit_img.png", "software": "EOM/GAJOE", "chi_square_value": 0.782, "p_value": 0.025315, "fit_residual_plot": "SASDEV2_fit1_fitresiduals_img.png", "fit_data": "https://www.sasbdb.org/media/fitting_files/SASDEV2_fit1.fit", "fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_HteiT4C.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 protein contains a penultimate non-canonical amino acid p-acetylphenylalanine (207 Da) that is represented as U (selenocysteine, 168 Da) in the amino acid sequence for the entry. Therefore, the calculated MW from sequence (MW(expected)) must be adjusted accordingly (ca. 40 Da).", "experiment_description": null, "tags": [ "idp" ], "intensity_unit": "arbitrary", "experimental_mw": 11.3, "experimental_mw_error": null, "guinier_i0_mw": null, "guinier_i0_mw_error": null, "porod_mw": null, "porod_mw_error": null, "pddf_i0": 1071.0, "pddf_i0_error": 5.5, "guinier_i0": 1059.5, "guinier_i0_error": 5.3, "pddf_rg": 2.651, "pddf_rg_error": 0.02, "guinier_rg": 2.49, "guinier_rg_error": 0.13, "pddf_dmax": 9.18, "pddf_dmax_error": null, "porod_volume": 14.97, "porod_volume_error": null, "estimated_volume": null, "estimated_volume_error": null, "guinier_point_first": 16, "guinier_point_last": 187, "pddf_point_first": null, "pddf_point_last": null, "i0_calibration_standard_data": null, "intensities_log_log_plot": "SASDEV2_datloglog_img.png", "symmetry": null, "last_modified": "2023-06-21T07:56:39.492710+02:00", "bragg_peak": [] }