S3 Text: Three additional test cases. Yannick G. Spill and Michael Nilges. Here, we report three additional test cases extracted from a recent SAXS bench- mark1.
S3 Text: Three additional test cases Yannick G. Spill and Michael Nilges
Here, we report three additional test cases extracted from a recent SAXS benchmark1 • ATG7: Ubiquitin-like modifier-activating enzyme, ATG7 C-terminal domain2 • PYR1P: Abscisic acid receptor PYR13 • SOD: Superoxide dismutase4
References Nishimura, Noriyuki, Kenichi Hitomi, Andrew S. Arvai, Robert P. Rambo, Chiharu Hitomi, Sean R. Cutler, Julian I. Schroeder, and Elizabeth D. Getzoff (2009). “Structural Mechanism of Abscisic Acid Binding and Signaling by Dimeric PYR1”. In: Science 326.5958, pp. 1373–1379. doi: 10.1126/science.1181829 (cit. on p. 1). Schneidman-Duhovny, Dina, Michal Hammel, John A. Tainer, and Andrej Sali (2013). “Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments”. In: Biophys. J. 105.4, pp. 962–974. doi: 10.1016/j.bpj.2013.07.020 (cit. on p. 1). Shin, David S., Michael DiDonato, David P. Barondeau, Greg L. Hura, Chiharu Hitomi, J. Andrew Berglund, Elizabeth D. Getzoff, S. Craig Cary, and John A. Tainer (2009). “Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis”. In: J. Mol. Biol. 385.5, pp. 1534–1555. doi: 10.1016/j.jmb.2008.11.031 (cit. on p. 1). Taherbhoy, Asad M., Stephen W. Tait, Stephen E. Kaiser, Allison H. Williams, Alan Deng, Amanda Nourse, Michal Hammel, Igor Kurinov, Charles O. Rock, Douglas R. Green, and Brenda A. Schulman (2011). “Atg8 Transfer from Atg7 to Atg3: A Distinctive E1-E2 Architecture and Mechanism in the Autophagy Pathway”. In: Mol. Cell 44.3, pp. 451–461. doi: 10.1016/j.molcel.2011.08.034 (cit. on p. 1). 1 Schneidman-Duhovny 2 Taherbhoy
et al. 2011. 3 Nishimura et al. 2009. 4 Shin et al. 2009.
et al. 2013.
1
Linear scale
Logarithmic scale ·10−2
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Figure 1: Mean (blue) and standard deviation (red) of the SAXS profile of three −1
different protein systems. X-axis is q(Å ). Left y-axis is SAXS intensity (A.U.), right y-axis is standard deviation (left panel, A.U.) or coefficient of variation V ≡ σ/µ (right panel).
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Figure 2: ATG7
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qi (Å−1 ) Figure 3: PYR1P
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qi (Å−1 ) Figure 4: sod
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