Dina Schneidman-Duhovny, Michal Hammel, John A. Tainer, Andrej Sali

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Presentation transcript:

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments Dina Schneidman-Duhovny, Michal Hammel, John A. Tainer, Andrej Sali Biophysical Journal Volume 105, Issue 4, Pages 962-974 (August 2013) DOI: 10.1016/j.bpj.2013.07.020 Copyright © 2013 Biophysical Society Terms and Conditions

Figure 1 Fit and residual plots for FoXS and CRYSOL: experimental data (dark gray), FoXS (red), and CRYSOL (green). The fit plots are for q(Å−1) (x axis) versus log-intensity (y axis). The residual plots are for q(Å−1) (x axis) versus experimental intensity divided by computed intensity (y axis). The cases are ordered by the number of atoms as in Tables 1 and 2. Biophysical Journal 2013 105, 962-974DOI: (10.1016/j.bpj.2013.07.020) Copyright © 2013 Biophysical Society Terms and Conditions

Figure 2 Comparison of FoXS and CRYSOL adjustable parameters and running times. (A) CRYSOL r0 versus c1. (B) CRYSOL δρ versus FOXS c2. (C) Running times of FoXS (red) versus CRYSOL (green) and CRYSOL L50 (dark green, order of harmonics = 50). Biophysical Journal 2013 105, 962-974DOI: (10.1016/j.bpj.2013.07.020) Copyright © 2013 Biophysical Society Terms and Conditions

Figure 3 Cross correlation of χ-scores with model accuracy. (A) Superoxide dismutase, (B) abscisic acid receptor PYR1, (C) ubiquitin-like modifier-activating enzyme ATG7 C-terminal domain, (D) DNA double-strand break repair protein MRE11, and (E) glucose isomerase. For each of the five cases, a set of models is shown, followed by the χ-scores versus model accuracy for FoXS, FoXS′, and CRYSOL. Biophysical Journal 2013 105, 962-974DOI: (10.1016/j.bpj.2013.07.020) Copyright © 2013 Biophysical Society Terms and Conditions

Figure 4 Salt concentration versus hydration layer density (δρ) for FoXS (red) and CRYSOL (green). (A and B) Glucose isomerase with KCl and NaCl, respectively. (C and D) Lysozyme with KCl and NaCl, respectively. Biophysical Journal 2013 105, 962-974DOI: (10.1016/j.bpj.2013.07.020) Copyright © 2013 Biophysical Society Terms and Conditions

Figure 5 The thickness of hydration layer based on crystal waters versus concentration for (A) lysozyme and (C) glucose isomerase. The thickness of hydration layer based on crystal waters versus hydration layer density (FoXS c2) for (B) lysozyme and (D) glucose isomerase. (Blue) NaCl; (red) KCl. Biophysical Journal 2013 105, 962-974DOI: (10.1016/j.bpj.2013.07.020) Copyright © 2013 Biophysical Society Terms and Conditions

Figure 6 Finding the minimal ensemble consistent with a SAXS profile. Ensemble fit (blue) of the SAXS data (black) versus single conformation fit (red) for (A) XLF-XRCC4 filaments and (C) ligase III-DNA complex. (B and D) Conformations and their weights in the minimal ensemble. Biophysical Journal 2013 105, 962-974DOI: (10.1016/j.bpj.2013.07.020) Copyright © 2013 Biophysical Society Terms and Conditions