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{
"code": "SASDCQ2",
"status": "Published",
"type_of_curve": "Other",
"angular_unit": "1/A",
"project": {
"title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.",
"publication": {
"title": "2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update.",
"author_list": "Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE",
"journal": "Acta Crystallogr D Struct Biol",
"doi": "10.1107/S2059798317011597",
"pmid": "28876235",
"published_date": "2017 Sep 1"
},
"status": "released",
"submitted_date": "2017-05-06",
"released_date": "2017-08-22"
},
"pddf_data": "https://www.sasbdb.org/media/p_of_R_files/SASDCQ2.out",
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"intensities_kratky_plot": "https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCQ2_kratky_img.png",
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"sascif_data": "https://www.sasbdb.org/media/sascif/sascif_files/SASDCQ2.sascif",
"experiment": {
"instrument": {
"detector": {
"type": "Dectris",
"name": "Pilatus 1M",
"resolution": 172.0
},
"name": "Australian Synchrotron",
"city": "Melbourne",
"country": "Australia",
"beamline_name": "SAXS/WAXS",
"beam_geometry": "Point",
"type_of_source": "X-ray synchrotron",
"point_source": true,
"line_collimation": null,
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"line_collimation_slitlength": null,
"line_collimation_integrationwidth": null,
"xray_energy": null,
"beam_profile_ah": null,
"beam_profile_al": null
},
"sample": {
"molecule": [
{
"long_name": "Calmodulin-1",
"short_name": "CaM",
"sequence": "ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK",
"organism": "Xenopus laevis",
"uniprot_code": "P0DP33",
"uniprot_range_first": 2,
"uniprot_range_last": 149,
"oligomerization": "monomer",
"molecular_type": "protein",
"uniprot_sequence": "MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG\nNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDE\nEVDEMIREADIDGDGQVNYEEFVQMMTAK",
"mw": 16.706,
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"number_molecules": 1,
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"deuteration": null,
"molecule_source": "biological",
"molecule_description": null
}
],
"buffer": {
"name": "25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3",
"concentration_unit": null,
"comment": "2 mM TCEP and 0.1% (.01538 M) NaN3 used for radiation protection",
"additive": null,
"concentration": null,
"pka": null,
"ph": 7.5,
"deuteration": null
},
"purity_method": null,
"name": "4Ca2+-calmodulin - Xenopus laevis",
"ext_coefficient": null,
"contrast": null,
"specific_vol": null,
"dry_vol": null,
"absorbption": null,
"deuteration": null,
"mixture": null
},
"contributor": [
{
"affiliation": [
{
"short_name": null,
"address": "Sydney, New South Wales 2006, Australia",
"full_name": "School of Molecular Bioscience, University of Sydney.",
"webpage": ""
}
],
"contributor_name": "Jill",
"contributor_surname": "Trewhella",
"orcid": null
}
],
"concentration_method": null,
"concentration_unit": null,
"date": "2017-03-09",
"storage_temperature": null,
"cell_temperature": 22.0,
"exposure_time": 1.0,
"number_of_frames": 24,
"wavelength": 0.10332,
"sample_detector_distance": 2.683,
"concentration_min": 0.74,
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"flow_rate": null,
"s_min": 0.066,
"s_max": 3.104,
"total_exposure_time": null,
"seccolumn": null
},
"fits": [
{
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{
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"software": "DAMMIN",
"pdb_link": [],
"model_title": null,
"type_of_model": "dummy",
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"bead_radius": 1.8,
"log": "https://www.sasbdb.org/media/log_files/CaMstder.log",
"symmetry": "P1",
"comment": "",
"user": 138
}
],
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"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCQ2_fit1_fixed_fit_img.png",
"software": "DAMMIN",
"chi_square_value": 0.844,
"p_value": 0.5326,
"fit_residual_plot": "SASDCQ2_fit1_fitresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCQ2_fit1.fir",
"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/CaMstder.log",
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{
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"ext_code": "1CLL",
"ext_type": "pdb",
"difference_with_model": "derived"
}
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"symmetry": "P1",
"comment": "Representative model from 1-state ensemble calculation, flexible residues 77-81",
"user": 138
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCQ2_fit2_fitfoxs_img.png",
"software": "MES-FoXS",
"chi_square_value": 0.85,
"p_value": 0.3144,
"fit_residual_plot": "SASDCQ2_fit2_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCQ2_fit2.dat",
"fit_log": null,
"software_version": "on-line",
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"software": "MultiFoXS",
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"ext_code": "1CLL",
"ext_type": "pdb",
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}
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"type_of_model": "atomic",
"software_version": "on-line",
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"model_mw": 16.84,
"bead_radius": 1.9,
"log": null,
"symmetry": "P1",
"comment": "Representative model-0 from 2-state ensemble, flexible residues 77-81",
"user": 138
},
{
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"software": "MultiFoXS",
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"difference_with_model": "derived"
}
],
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"software_version": "on-line",
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"log": null,
"symmetry": "P1",
"comment": "Representative model-1 from 2-state ensemble, flexible residues 77-81",
"user": 138
}
],
"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCQ2_fit3_fitfoxs_img.png",
"software": "MES-FoXS",
"chi_square_value": 0.79,
"p_value": 0.7877,
"fit_residual_plot": "SASDCQ2_fit3_fitfoxsresiduals_img.png",
"fit_data": "https://www.sasbdb.org/media/fitting_files/SASDCQ2_fit3.dat",
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"software_version": "on-line",
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},
{
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"fit_unit": "1/A",
"fit_plot": "https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCQ2_fit4_fixed_fit_img.png",
"software": "EOM/GAJOE",
"chi_square_value": 0.815,
"p_value": 0.7877,
"fit_residual_plot": "SASDCQ2_fit4_fitresiduals_img.png",
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"fit_log": "https://www.sasbdb.org/media/fitting_files/log_files/logFile_001_1_e5c7X78.log",
"software_version": null,
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}
],
"estimated_volume_method": null,
"pddf_software": "ATSAS GNOM",
"pddf_software_version": "GNOM",
"i0_calibration_standard": null,
"description": null,
"experiment_description": "Synchrotron SAXS data from solutions of calcium-loaded calmodulin in 25 mM MOPS, 250 mM NaCl, 50 mM KCl, 2 mM TCEP, 0.1% NaN3, pH 7.5 were collected on the SAXS/WAXS beam line at Australian Synchrotron (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 2.7 m and at a wavelength of λ = 0.10332 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Scattering data are on an absolute scale (cm-1) set by reference to the scattering from pure H2O at 22°C. I(0) values must be corrected for the shear flow sample cell by a 2.05 multiplicative factor. Data were acquired in SEC-SAXS mode, summed from 12 x 1 second measurement frames where Rg was flat and at a maximum. The average concentration over the frames was 0.959 mg/mL, spanning values from 0.74 - 1.1 mg/mL. Sample concentrations were measured by A280 (extinction coefficient for 1 mg/mL, 10 mm pathlength; E0.1% = 0.178), corrected for the 3.1 mm path-length of the UV measurement cell. MULCh was used to calculate the partial specific volume (0.716 mL/g) and X-ray contrast (Δρ = 3.093e10 cm-2). The protein is a monomer in the solution conditions measured, experimental molecular weight provided includes the 4 bound calcium ions. The multi-state (Multi-FoXS, 1-state and 2-sate fits) and ensemble model (EOM, lower panel) fits to the data assumed flexibility in residues 77-81, the region identified by NMR relaxation as highly mobile in the helix connecting the N- and C-terminal CaM domains. The distribution of Rg values shown for the EOM fit represents the pool (gray) and the optimized ensemble (blue).",
"tags": [
"benchmark"
],
"intensity_unit": "1/cm",
"experimental_mw": 16.842,
"experimental_mw_error": null,
"guinier_i0_mw": 22.003,
"guinier_i0_mw_error": null,
"porod_mw": 16.8,
"porod_mw_error": null,
"pddf_i0": 0.02667,
"pddf_i0_error": 0.0003,
"guinier_i0": 0.027,
"guinier_i0_error": 2.5e-05,
"pddf_rg": 2.219,
"pddf_rg_error": 0.003,
"guinier_rg": 2.174,
"guinier_rg_error": 0.006,
"pddf_dmax": 7.22,
"pddf_dmax_error": null,
"porod_volume": 25.2,
"porod_volume_error": null,
"estimated_volume": null,
"estimated_volume_error": null,
"guinier_point_first": 2,
"guinier_point_last": 69,
"pddf_point_first": null,
"pddf_point_last": null,
"i0_calibration_standard_data": null,
"intensities_log_log_plot": "SASDCQ2_datloglog_img.png",
"symmetry": null,
"last_modified": "2023-03-03T13:30:53.110509+01:00",
"bragg_peak": []
}
