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Statistics common problems with SAXS samples



See Beamline Publications


Most Common sample problems % of samples


Publications


2013

Perry JJ, Tainer JA. Methods. 2013 Mar 1;59(3):363-71. doi:10.1016/j.ymeth.2013.01.005. Epub 2013 Jan 29.


2012

Luebbering, E.K., Mick, J., Singh, R.K., Tanner, J.J., Mehra-Chaudhary, R., and Beamer, L.J. "Conservation of Functionally Important Global Motions in an Enzyme Superfamily across Varying Quaternary Structures." J Mol Biol. (Aug, 2012)

Lyubimov, A.Y., Costa, A., Bleichert, F., Botchan, M.R., and Berger, J.M. "ATP-dependent conformational dynamics underlie the functional asymmetry of the replicative helicase from a minimalist eukaryote." Proceedings of the National Academy of Sciences 109, 11999–12004. (July 24, 2012)

Hilario, E., Li, Y., Niks, D., and Fan, L. "The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property." Acta Crystallogr D Biol Crystallogr 68, 846–853.

Zheng, Y., Kim, S.H., Patel, A.B., Narayanaswami, V., Iavarone, A.T., Hura, G.L., and Bielicki, J.K. "The Positional Specificity of EXXK Motifs within an Amphipathic α-Helix Dictates Preferential Lysine Modification by Acrolein: Implications for the Design of High-Density Lipoprotein Mimetic Peptides." Biochemistry, 51 (32), pp 6400–6412 (July 2012)

Logsdon, N.J., Deshpande, A., Harris, B.D., Rajashankar, K.R., and Walter, M.R. "Structural basis for receptor sharing and activation by interleukin-20 receptor-2 (IL-20R2) binding cytokines." Proceedings of the National Academy of Sciences 109, 12704–12709. (June 2012)

Jenkins, J.L., Laird, K.M., and Kielkopf, C.L. "A Broad Range of Conformations Contribute to the Solution Ensemble of the Essential Splicing Factor U2AF(65)." Biochemistry, 51 (26), pp 5223-5224 (June 19, 2012)

Burke, J.R., Hura, G.L., and Rubin, S.M. "Structures of inactive retinoblastoma protein reveal multiple mechanisms for cell cycle control." Genes Dev. (May 2012)

>Ru, H., Zhao, L., Ding, W., Jiao, L., Shaw, N., Liang, W., Zhang, L., Hung, L.-W., Matsugaki, N., Wakatsuki, S., et al. "S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS." Acta Crystallogr D Biol Crystallogr 68, 521–530. (May 2012)

Ruigrok, V.J.B., van Duijn, E., Barendregt, A., Dyer, K., Tainer, J.A., Stoltenburg, R., Strehlitz, B., Levisson, M., Smidt, H., and van der Oost, J. "Kinetic and stoichiometric characterisation of streptavidin-binding aptamers." Chembiochem 13, 829–836. (April 2012)

Dhatwalia, R., Singh, H., Oppenheimer, M., Karr, D.B., Nix, J.C., Sobrado, P., and Tanner, J.J. "Crystal structures and small-angle x-ray scattering analysis of UDP-galactopyranose mutase from the pathogenic fungus Aspergillus fumigatus." J Biol Chem 287, 9041–9051. (March 16, 2012)

Bétous, R., Mason, A. C., Rambo, R. P., Bansbach, C. E., Badu-Nkansah, A., Sirbu, B. M., Eichman, B. F., Cortez, D. "SMARCAL1 catalyzes fork regression and Holliday junction migration to maintain genome stability during DNA replication." Genes Dev, 26(2), 151–162.

Williams, C. K., Vaithiyalingam, S., Hammel, M., Pipas, J., & Chazin, W. J. "Binding to retinoblastoma pocket domain does not alter the inter-domain flexibility of the J domain of SV40 large T antigen." Archives of biochemistry and biophysics, 518(2), 111–118.

Bauer, W.J., Heath, J., Jenkins, J.L., and Kielkopf, C.L. "Three RNA recognition motifs participate in RNA recognition and structural organization by the pro-apoptotic factor TIA-1." J Mol Biol 415, 727–740. (Jan. 2012)


2011

Singh RK, Larson JD, Zhu W, Rambo RP, Hura GL, Becker DF, Tanner JJ. "Small-Angle X-ray Scattering Studies of the Oligomeric State and Quaternary Structure of the Trifunctional Proline Utilization A (PutA) Flavoprotein from Escherichia coli." J Biol Chem 2011 Oct.

Tsutakawa SE, Van Wynsberghe AW, Freudenthal BD, Weinacht CP, Gakhar L, Washington MT, Zhuang Z, Tainer JA, Ivanov I. "Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA." Proc Natl Acad Sci U S A. 2011 Oct 17.

Mehra-Chaudhary R, Mick J, Tanner JJ, Beamer LJ. "Quaternary structure, conformational variability and global motions of phosphoglucosamine mutase." FEBS J. 2011 Sep.;278(18):3298–3307.

Batchelor JD, Zahm JA, Tolia NH. "Dimerization of Plasmodium vivax DBP is induced upon receptor binding and drives recognition of DARC." Nat Struct Mol Biol 2011 Aug.;18(8):908–914.

Libeu CP, Poksay KS, John V, Bredesen DE. "Structural and functional alterations in amyloid-β precursor protein induced by amyloid-β peptides." J. Alzheimers Dis. 2011;25(3):547–566.

Fang P, Zhang HM, Shapiro R, Marshall AG, Schimmel P, Yang XL, Guo M. "Structural context for mobilization of a human tRNA synthetase from its cytoplasmic complex." Proceedings of the National Academy of Sciences 2011 May;108(20):8239–8244.

Zheng Y, Patel AB, Narayanaswami V, Hura GL, Hang B, Bielicki JK. "HDL mimetic peptide ATI-5261 forms an oligomeric assembly in solution that dissociates to monomers upon dilution." Biochemistry. 2011 May 17;50(19):4068-76. Epub 2011 Apr 20.

Gupta A, Jenkins JL, Kielkopf CL. "RNA induces conformational changes in the SF1/U2AF65 splicing factor complex." J Mol Biol 2011 Feb.;405(5):1128–1138.


2010

Tonthat NK, Arold ST, Pickering BF, Van Dyke MW, Liang S, Lu Y, Beuria TK, Margolin W, Schumacher MA. "Molecular mechanism by which the nucleoid occlusion factor, SlmA, keeps cytokinesis in check." EMBO J. 2011 Jan 5;30(1):154-64. Epub 2010 Nov 26.

Gatzeva-Topalova, P.Z., Warner, L.R., Pardi, A., and Sousa, M.C. "Structure and flexibility of the complete periplasmic domain of BamA: the protein insertion machine of the outer membrane." Structure 18, 1492–1501.

Stoddard CD, Montange RK, Hennelly SP, Rambo RP, Sanbonmatsu KY, Batey RT. "Free state conformational sampling of the SAM-I riboswitch aptamer domain." Structure 2010 Jul.;18(7):787–797.

Habel, J.E., Bursey, E.H., Rho, B.-S., Kim, C.-Y., Segelke, B.W., Rupp, B., Park, M.S., Terwilliger, T.C., and Hung, L.-W. "Structure of Rv1848 (UreA), the Mycobacterium tuberculosis urease gamma subunit." Acta Crystallogr Sect F Struct Biol Cryst Commun 66, 781–786. (July 2010).

Pretto DI, Tsutakawa S, Brosey CA, Castillo A, Chagot ME, Smith JA, Tainer JA, Chazin WJ. "Structural dynamics and ssDNA binding activity of the three N-terminal domains of the large subunit of Replication Protein A from small angle X-ray scattering." Biochemistry. 2010 Feb 25. [Epub ahead of print]

Iyer RR, Pluciennik A, Genschel J, Tsai MS, Beese LS, Modrich P. "MutLα and proliferating cell nuclear antigen share binding sites on Mutsβ" J Biol Chem. 2010 Feb 16.