[RASMB] a hiccup in radial space

Leech, AP apl3 at york.ac.uk
Thu Dec 18 11:59:52 PST 2008


Hi Chad,

If it is a sticky rail, wouldn't you expect a flattened part of the
scan before the jump?

Can you check the intensity and incident data in the same region
and on an empty hole (if available)? (and if it is an XL/I does
the jump show up in the interference optics?)

It might be interesting to analyse the regions before and after the
jump separately to see if they are consistent. I'm not sure I'd trust
it though.

I wonder if it could be something in the monochromator? 400 nm filter
out of position perhaps?

Andrew


Chad Brautigam wrote:
> Dear All,
> 
> Whilst checking the data from the first speed of a sedimentation 
> equilibrium run, I noticed a troubling discontinuity in the data.  It 
> appears in all three cells, and it is not exactly subtle.  The jump in 
> the data can be as much as 0.1 OD, and it always occurs betwixt 7.05 and 
> 7.06 in radial space.  The anomaly occurs at both 280 and 250 nm.  I 
> attach a graph of three successive scans from the same cell, spaced four 
> hours apart, for your delectation.  The data were collected in stepping 
> mode, with 20 replicates.
> 
> While I suspect that the heavily glycosylated protein in these samples 
> might behave nonideally, I suspect that the real problem here is 
> instrumentation, maybe a sticky rail.  But, before calling my service 
> rep, I thought I'd tap the collective wisdom of the AUC hive mind.
> 
> And a further question:  do y'all think that these data can still be 
> analyzed if I simply exclude the affected region from the analysis?  I'm 
> running in the 6-hole centerpieces, so that means I'd be eliminating 
> about half of the data from the outer holes.  Alas.
> 
> Thanks for any insight you can provide.
> 
> Best,
> Chad
> 
> 
> 
> 
> ======================================
> Chad A. Brautigam, Ph.D.
> Assistant Professor
> Department of Biochemistry
> The University of Texas
> Southwestern Medical Center at Dallas
> Department of Biochemistry
> 5323 Harry Hines Blvd.
> Rm. ND10.214G
> Dallas, TX 75390-8816
> Office:  214-645-6384
> Fax:  214-645-6353
> Email:  chad.brautigam at utsouthwestern.edu
> 
> 
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-- 
Dr Andrew Leech                   *  Laboratory Manager
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