Bioisis

"Median and Mean Xylanase Data"

Experimental SAS Curve

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Experimental Mass

21,000 Da

Experimental Details for BID:  1XYNTP
Experiment ID: 78
Collected at: ALS BL 12.3.1
Contributors: Rambo, RP
High noise dataset used to demonstrate propagation of error and influence of noise on Chi-square. 10 independent, 5 sec exposures of size-exclusion chromatography purified xylanase collected to qmax = 0.31 (Å-1) at ~1.4 mg/ml. Median SAS curve is the median intensity for each I(q). Intensities and associated uncertainties that are taken as the median best approximate the average I(q) without signal enhancement from averaging. Model fits with CRYSOL to PDB: 1REF produced a chi2 of 0.995 and chi2free of 1.66. Average SAS curve is the average intensity for each I(q). Model fits with CRYSOL produced a conventional chi2 of 1.00 and chi2free of 1.56.
single concentration. Sample was divided into 10 separate wells with 10 different buffers.

Electron Pair Distribution

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       Dmax → 43 Å


Guinier Plot

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     Guinier Rg → 16.74 Å

Real Space Rg → 15.96 Å

The Guinier plot is used to estimate the radius of gyration, Rg, which is taken from the slope of a line observed at low scattering angles (typically in the range where q* Rg < 1.3). This should be in reasonable agreement with the real space Rg.


Kratky Plot

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The Kratky plot can be used to visually assess the degree of "unfoldedness" of a protein or RNA sample. The plot of a well-behaved folded protein approaches the baseline at high q values creating a parabolic shape.


PDB Model fit to SAXS Data

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The red line is the calculated SAXS profile from a PDB model scaled to the experimental SAXS curve (cyan). The two curves agree with a Chi2 of 1.6.


Additional Experimental Details
Title

Median and Mean Xylanase Data

Description

High noise dataset used to demonstrate propagation of error and influence of noise on Chi-square. 10 independent, 5 sec exposures of size-exclusion chromatography purified xylanase collected to qmax = 0.31 (Å-1) at ~1.4 mg/ml. Median SAS curve is the median intensity for each I(q). Intensities and associated uncertainties that are taken as the median best approximate the average I(q) without signal enhancement from averaging. Model fits with CRYSOL to PDB: 1REF produced a chi2 of 0.995 and chi2free of 1.66. Average SAS curve is the average intensity for each I(q). Model fits with CRYSOL produced a conventional chi2 of 1.00 and chi2free of 1.56.

Publication

Accurate assessment of mass, models and resolution by small-angle scattering. Nature. 2013 Apr 25;496(7446):477-81.

Contributors

Rambo, RP

Genomics and Proteomics

The experiment is composed of a single gene/ORF

Abbreviated name: XYNAT1

Annotation: Xylanase. sequence. from. 1REF

ETIQPGTGYN NGYFYSYWND GHGGVTYTNG PGGQFSVNWS NSGNFVGGKG WQPGTKNKVI NFSGSYNPNG NSYLSVYGWS RNPLIEYYIV ENFGTYNPST GATKLGEVTS DGSVYDIYRT QRVNQPSIIG TATFYQYWSV RRNHRSSGSV NTANHFNAWA QQGLTLGTMD YQIVAVEGYF SSGSASITVS
categoryamino acid composition(%)
HydrophobicI(4.7) V(7.4) L(2.6) M(0.5) A(3.7) G(14.2) P(3.7)
AromaticF(4.2) W(3.2) Y(8.9)
HydrophilicR(3.2) K(2.1) E(2.6) D(2.1) Q(4.7) N(10.5) H(1.6) S(11.6) T(8.4) C(0.0)