The following content comes directly from the SASBDB entry. Missing values are shown as “—”; SAXSdb does not infer undeclared units.
Every source field is expanded here, including empty values, list members and fields already shown above.
View the complete summary.json source
{
"code": "SASDCB2",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/A",
"project": {
"title": "A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.",
"publication": {
"title": "A homologue of the Parkinson's disease-associated protein LRRK2 undergoes a monomer-dimer transition during GTP turnover.",
"author_list": "Deyaert E, Wauters L, Guaitoli G, Konijnenberg A, Leemans M, Terheyden S, Petrovic A, Gallardo R, Nederveen-Schippers LM, Athanasopoulos PS, Pots H, Van Haastert PJM, Sobott F, Gloeckner CJ, Efremov R, Kortholt A, Versées W",
"journal": "Nat Commun",
"doi": "10.1038/s41467-017-01103-4",
"pmid": "29044096",
"published_date": "2017 Oct 18"
},
"status": "released",
"submitted_date": "2017-03-21",
"released_date": "2017-10-20"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCB2.out",
"intensities_data": "https://www.sasbdb.org/media/intensities_files/SASDCB2.dat",
"intensities_log_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCB2_dat_img.png",
"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCB2_kratky_img.png",
"pddf_plot": "https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCB2_pofr_img.png",
"intensities_guinier_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCB2_guinier_img.png",
"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCB2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "CCD",
"name": "AVIEX PCCD170170",
"resolution": null
},
"name": "SOLEIL",
"city": "Saint-Aubin",
"country": "France",
"beamline_name": "SWING",
"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": "Rab family protein",
"short_name": null,
"sequence": "> C.t. RocCOR412-946\r\nMSYYHHHHHHDYDIPTTENLYFQGAMGSDNPLESPPPEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPKESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLLDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISCKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICNDSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLNTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEGALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDELVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKER",
"organism": "Chlorobaculum tepidum",
"uniprot_code": "Q8KC98",
"uniprot_range_first": null,
"uniprot_range_last": null,
"oligomerization": "dimer",
"molecular_type": "protein",
"uniprot_sequence": "MSDLDVIRQIEQELGMQLEPVDKLKWYSKGYKLDKDQRVTAIGLYDCGSDTLDRIIQPLE\nSLKSLSELSLSSNQITDISPLASLNSLSMLWLDRNQITDIAPLASLNSLSMLWLFGNKIS\nDIAPLESLKSLTELQLSSNQITDIAPLASLKSLTELSLSGNNISDIAPLESLKSLTELSL\nSSNQITDIAPLASLKSLTELSLSSNQISDIAPLESLKSLTELQLSRNQISDIAPLESLKS\nLTELQLSSNQITDIAPLASLKSLTELQLSRNQISDIAPLESLNSLSKLWLNGNQITDIAP\nLASLNSLTELELSSNQITDIAPLASLKSLSTLWLSSNQISDIAPLASLESLSELSLSSNQ\nISDISPLASLNSLTGFDVRRNPIKRLPETITGFDMEILWNDFSSSGFITFFDNPLESPPP\nEIVKQGKEAVRQYFQSIEEARSKGEALVHLQEIKVHLIGDGMAGKTSLLKQLIGETFDPK\nESQTHGLNVVTKQAPNIKGLENDDELKECLFHFWDFGGQEIMHASHQFFMTRSSVYMLLL\nDSRTDSNKHYWLRHIEKYGGKSPVIVVMNKIDENPSYNIEQKKINERFPAIENRFHRISC\nKNGDGVESIAKSLKSAVLHPDSIYGTPLAPSWIKVKEKLVEATTAQRYLNRTEVEKICND\nSGITDPGERKTLLGYLNNLGIVLYFEALDLSEIYVLDPHWVTIGVYRIINSSKTKNGHLN\nTSALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNL\nPTQIDNEPEITEGEPLRFIMKYDYLPSTIIPRLMIAMQHQILDRMQWRYGMVLKSQDHEG\nALAKVVAETKDSTITIAIQGEPRCKREYLSIIWYEIKKINANFTNLDVKEFIPLPGHPDE\nLVEYKELLGLEKMGRDEYVSGKLEKVFSVSKMLDSVISKEERNKERLMGDINIKLENIGN\nPTIPIHQQVEVNVSQETVQHVENLQGFFENLKADILREAELEIDDPKERKRLANELELAE\nNAITKMDAAVKSGKNKLKPDVKDRLGEFIDNLANENSRLRKGIALVMNGAEKVQKLARYY\nNNVAPFFDLPSVPPVLLGKEKT",
"mw": 64.865,
"total_mw": 129.73,
"number_molecules": 2,
"complex_state": false,
"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT",
"concentration_unit": null,
"comment": null,
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "Rab family protein CtRoc-COR nucleotide free",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": "VUB",
"address": "Pleinlaan 2 1050 Brussel ",
"full_name": "Vrije Universiteit Brussel",
"webpage": "http://www.vub.ac.be/"
}
],
"contributor_name": "Egon",
"contributor_surname": "Deyaert",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-02-01",
"storage_temperature": null,
"cell_temperature": 25.0,
"exposure_time": 0.75,
"number_of_frames": 31,
"wavelength": 0.103,
"sample_detector_distance": null,
"concentration_min": 1.0,
"concentration_max": 2.0,
"sample_volume": null,
"flow_rate": null,
"s_min": 0.04,
"s_max": 6.134,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCB2_fit1_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/SASDCB2_fit1_model1.pdb",
"model_mw": 120.6,
"bead_radius": 3.25,
"log": "https://www.sasbdb.org/media/log_files/refine_ATjpN82.log",
"symmetry": "P2",
"comment": "",
"user": 98
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCB2_fit1_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.797,
"p_value": 0.0,
"fit_residual_plot": "SASDCB2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCB2_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/refine_yw857M4.log",
"software_version": "5.3",
"description": null
},
{
"models": [
{
"model_plot": "https://www.sasbdb.org/media/pdb_file/images/SASDCB2_fit2_model1_img.png",
"software": "CORAL",
"pdb_link": [
{
"pdb_code": "3dpu",
"ext_code": "3DPU",
"ext_type": "pdb",
"difference_with_model": "derived"
}
],
"model_title": null,
"type_of_model": "mix",
"software_version": "",
"model_data": "https://www.sasbdb.org/media/pdb_file/SASDCB2_fit2_model1.pdb",
"model_mw": 117.1,
"bead_radius": 1.9,
"log": "https://www.sasbdb.org/media/log_files/C_RcCR_200.log",
"symmetry": "P2",
"comment": "",
"user": 98
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCB2_fit2_fit_img.png",
"software": "CRYSOL",
"chi_square_value": 0.896,
"p_value": 0.0,
"fit_residual_plot": null,
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCB2_fit2.fit",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/C_RcCR_200.log",
"software_version": "2.8.3",
"description": null
}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM 4.6",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of Rab family protein CtRoc-COR (nucleotide free) in 20 mM HEPES 150 mM NaCl 5 mM MgCl2 5% Glycerol 1 mM DTT, pH 7.5 were collected on the SWING camera on the storage ring SOLEIL (Saint-Aubin, France) using a CCD AVIEX detector at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsin θ/λ and 2θ is the scattering angle). Inline SEC-SAXS was employed at 25°C (50 µl injection volume of an 8 mg/ml protein solution on a Bio SEC-3 HPLC column (Agilent, 3 µm 300 Å)). 31 successive 0.750 second frames were collected through the elution peak. 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 and averaged to produce the final SAXS data displayed in this entry.",
"tags": [],
"intensity_unit": null,
"experimental_mw": 120.0,
"experimental_mw_error": null,
"guinier_i0_mw": null,
"guinier_i0_mw_error": null,
"porod_mw": 124.0,
"porod_mw_error": null,
"pddf_i0": 0.09434,
"pddf_i0_error": 2.824e-05,
"guinier_i0": 0.094844,
"guinier_i0_error": 4.15e-05,
"pddf_rg": 3.362,
"pddf_rg_error": 0.002,
"guinier_rg": 3.41,
"guinier_rg_error": 0.003,
"pddf_dmax": 10.0,
"pddf_dmax_error": null,
"porod_volume": 210.78,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 15,
"guinier_point_last": 60,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCB2_datloglog_img.png",
"symmetry": null,
"last_modified": "2020-07-03T15:07:28.841012+02:00",
"bragg_peak": []
}
