[3dem] 答复: Resolution estimate: FSC vs PDB modeling

[Hongwei Wang]

Hi, Qiu-Xing,

 

You may want to try the method that Richard Henderson and his colleagues
described most recently in their Ultramicrosopy paper:
http://www.ncbi.nlm.nih.gov/pubmed/23872039

 

Best,

Hongwei 

 

发件人: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu] 代
表 Qiu-Xing Jiang
发送时间: 2014年3月12日 20:47
收件人: 3dem at ncmir.ucsd.edu
主题: Re: [3dem] Resolution estimate: FSC vs PDB modeling

 

Dear colleagues, 

This has been a topic discussed in a couple of map validation papers. I have
a scenario encountered in a recent project and would like some input from
those interested. 

We had a filament complex reconstruction, made of a small protein whose
crystal structure contains mainly loops held together in the core by three
pairs of disulfide bonds. At the time of resolution estimation, we used two
independent maps calculated from either randomly selected halves or
top/bottom halves to calculate FSC as usual in SPIDER. The FSC0.5 of the
former gives 9.2 angstroms, which is more conservative than the FSC0.143 of
the latter, and was used as a nominal estimate. 

 

The other opinion  from a senior colleague was PDB modeling, whose
operations are to dock the X-ray structures of individual units into the map
(assuming no change), filter the resulted PDB model to different
resolutions, and visually determine at which resolution the map calculated
from the PDB model and the experimental density map match the best(at
certain thresholds), and could then be used for resolution estimate. When we
were operating this procedure, we knew that our filaments had lipids
associated and our map was not good enough to resolve the loops on the
surface of the individual units in the filament. To make  the two maps match
well to our eyes, we had to filter both to 12-15 angstroms, which would then
say the resolution was 12-15 A. The calculated cross-correlation between the
map from the pdb model and the experimental map was high at 9.2-15 range,
but we were not sure whether it would be decisively meaningful. 

 

We had debates and disagreements on which to report. At the end we decided
to use FSC0.5 as usual, and refrained from interpreting the map with
mutations at the subunit interface due to the experience of PDB modeling. I
wonder if some of you had similar experience, and more generally whether PDB
modeling is suitable to replace FSC. 

 

Thanks for sharing your experience. 

 

Best regards,

 

Qiu-Xing

 

 

 

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UT Southwestern Medical Center
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