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CCP4BB  February 2011

CCP4BB February 2011

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Subject:

Re: First images of proteins and viruses caught with an X-ray laser

From:

James Holton <[log in to unmask]>

Reply-To:

James Holton <[log in to unmask]>

Date:

Thu, 10 Feb 2011 12:05:44 -0800

Content-Type:

text/plain

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text/plain (56 lines)

I hope everyone understands that I am not the corresponding author on 
this paper!  That is Henry Chapman.  He, and most of the other authors 
have been slaving away on this problem for most of their professional 
careers.  To be honest, I never did think it was going to work, and I 
was absolutely "gobsmacked" as they say when I heard they got spots 
going all the way out to the edge of the detector!

However, since my involvement was mostly about the data processing and 
refinement, I think Henry won't mind if I respond to a few of the 
questions posted on the BB about it.

Hudel:

Hmm.  Looks like our paper didn't report the R/Rfree for the "control" 
data set.  Crap.  Sorry about that.  For the "record", it was 
0.27/0.30.  These "control" data were collected from a large and 
cryo-cooled photosystem I crystal at ALS 8.2.2, truncated to 8.5 A and 
artificially "twinned" by averaging F(h,k,l)^2 and F(k,h,-l)^2, then 
subjected to the same rigid-body REFMAC refinement as the LCLS data.  
Exactly the same Rfree flags were used for both cases, and these were 
chosen in the point group 622 so that no "twin mates" were in both the 
working and test sets.

And before you ask, no, I have no idea why the "control" data were 
"worse".  However, I can say that they were not all that different from 
the LCLS data.  The maps (which were shown) don't really look all that 
different (IMHO), and the R-iso between the ALS and LCLS datasets was 
22% (also shown).  I thought the latter was amazing agreement 
considering that the ALS crystal was cryo-cooled, the LCLS crystals were 
at room temperature and the lowest R-iso between lysozyme datasets in 
the PDB collected at room temp vs cryo is 20% (2hu1 vs 2epe).  Yes, I 
checked all 10,000 lysozyme-lysozyme pairings.

I'm afraid I can't directly address Hudel's Rtwin = 0.7*Rnormal rule 
because de-twinned LCLS data are not yet available and I don't have the 
untwinned ALS data on my computers.  The reason I was "impressed" was 
because data in this resolution range generally don't fit very well to 
molecular models (have a look at R/Rfree in the infinity-9A bin of your 
last structure).  So, I was surprised to see that R/Rfree was "okay".  I 
guess I am just a pessimist.  All I can really say is that we used 
Refmac_5.6.0076, and the data are deposited under 3pcq if anyone wants 
to play with it.

-James Holton
MAD Scientist

On 2/9/2011 10:28 PM, Hudel Luecke wrote:
> James,
>
> I must admit not (yet) having read the "data processing paper PMID: 20389587" nor the 88 author paper.  Nevertheless, I would like to comment on your remark "Personally, I was quite impressed by how good the R factors were, all things considered."
>
> If I am not mistaken, perfectly twinned intensity data, such as you seem to have been dealing with, will generate data sets with compressed dynamic ranges, which in turn means that crystallographic R factors computed based on such data sets will be lower by roughly sqrt(2) or 1.4 compared to a non-twinned data set.  So a somewhat iffy R(cryst) of 30% would look quite nice (21.4%) when computed on a hemihedrally twinned data set.  But maybe this is all discussed in your paper...
>
>
> Cheers, Hudel
>

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