This is a reply to the below message posted under "[ccp4bb] The
importance of USING our validation tool", which is a rather long thread now.
I worked with Lars Pedersen on a rather high (78%) solvent content
crystal, 1VKJ. The interesting thing is that there are 3 molecules in
the AU, with 2 well-defined, and one that is almost invisible. Without
the 3rd molecule, it looks like tubes of protein floating in space with
no contacts. Here is the unit cell:
http://joekrahn.homelinux.com/top_ABC.png
The third molecule (chain C) is yellow, and is poorly ordered. You can
get a good R-factor with just the A and B molecules, but the cell looks
like this:
http://joekrahn.homelinux.com/top_AB.png
Molecule C forms tringular "girder" pattern seen here:
http://joekrahn.homelinux.com/side.png
Each brace across the girder pattern is 2 C molecules, which make
end-to-end contacts that are strong, but poor side-to-side stability.
This results in a fairly blurry, wobbly molecule, that still is strong
length-wise, which is all that is required for a strong girder system.
However, only the very ends are well ordered, and needs NCS restraints
against the A and B chains to be refined. If the had been an unknown
molecule, we could have a good result for molecules A and B, but
"floating" in space, with 86% solvent. I wonder if some other
high-solvent crystal is like this, where an unmodelled molecule can be
too poorly odered to model, but still supply enough strength along one
direction that it allows the crystal to be well-ordered.
Joe Krahn
Jenny Martin wrote:
> I've been reading the contributions on this topic with much interest.
> It's been very timely in that I've been giving 3rd year u/g lectures on
> protein X-ray structures and their validation over the past week.
> As part of the preparation for the lectures, I searched the PDB for
> structures with high solvent content.
> To my surprise, I found 376 crystal structures with solvent content >75%
> (about 1% of all crystal structures) and 120 structures with solvent
> content > 80% (about 0.3% of all crystal structures)
> However, there were only 3 other structures that (like 2HR0) had >80%
> AND Rcryst Rfree less than 20%. All three structures are solved to
> better than 3A Resolution.
> One is from a weak data set from a virus crystal, the other two PDB
> files report very strong crystallographic data.
> The Rmerge values are more typical than for 2HR0 and none of the three
> appear to have the geometry or crystal contact problems of 2HR0.
>
> My question is, how could crystals with 80% or more solvent diffract so
> well? The best of the three is 1.9A resolution with I/sigI 48 (top shell
> 2.5). My experience is that such crystals diffract very weakly.
> There are another 15 structures with solvent content 75-80% and
> Rcryst/Rfree < 20%. I didn't check them in any detail, just to see that
> the structure was consistent with a high solvent content.
>
> Any thoughts?
>
> Cheers,
> Jenny
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