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CCP4BB  June 2018

CCP4BB June 2018

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Subject:

Re: Please share your experience about "ugly" crystals showing good diffraction

From:

Debanu Das <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Thu, 28 Jun 2018 23:35:50 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (80 lines)

Hi Anirban,

At JCSG, we subjected ~180,000 crystals from ~3500 unique/novel
proteins/complexes to X-ray diffraction screening, resulting in >1500
novel structures in the PDB at an average resolution ~2.0A. In theory,
if we had the bandwidth now to sort through all that data to pull out
images of the mounted crystals and their diffraction quality, we could
probably get some good analysis done on this.

However, as an alternative, I can certainly provide some examples that
we have dealt with recently that I hope will add substance to the
anecdotes to motivate your trainees!

a) For one protein, our first crystals were oval shaped, without sharp
geometry/edges, much like a pebble. We got a high quality 1.9A
structure out of it. Subsequent optimization led to much nicer looking
crystals with nice shapes and we collected ~50 data sets from them all
resulting in ~2A structures so not much improved compared to the
initial visually poorer crystals.

b) For another protein, crystals grow nicely but some of the crystals
remain suspended in solution whereas other settle to the bottom and
stick. For the ones which stick, some can be dislodged by gentle
prodding with a nylon loop while harvesting and they result in (along
with the ones that are not stuck) in ~1.8-2A structures. For the ones
which are stuck and cannot be gently dislodged, a nudge with a plastic
tip (out of desperation!) is sufficient to dislodge them, and they
retain their nice visual appearance and shape, but have total loss in
diffraction.

c) We see this too for crystals soaked with ligands. In some cases
after soaking the crystals appear fine but suffer in diffraction
quality, and in some cases they appear to have suffered visually but
result in usable data sets/structures.

So at the end of the day there are crystals that appear nice but do
not diffract well and there are crystals that do not appear nice but
lead to good/usable structures. So it's all about inner beauty. Never
give up on crystals/crystal optimization without testing them by
X-rays.

Best,
Debanu

On Thu, Jun 28, 2018 at 5:07 PM, Anirban Banerjee <[log in to unmask]> wrote:
>
> Dear all,
>
> Apologies for the non-CCP4 related question.
>
> If you have concrete experience about visually unappealing, i.e. ugly
> crystals ( your own take on ugly is fine)  diffracting better than
> comparably similar sized nicer looking crystals of the same protein, will
> you please share here ? Even better if that led to a published structure.
> Might you also have pictures ?
>
> We have all heard anecdotes about not using visual appearance to judge the
> quality of crystals as far as their ability to give good diffraction data is
> concerned but I am trying to gather some concrete pointers here to motivate
> trainees.
>
> Thanks very much for any help.
>
> Best,
>
> Anirban
>
> P.S. I know that there is probably a lot of thought and wisdom  on this this
> specific topic but I am really looking for actual experience.
>
> ________________________________
>
> To unsubscribe from the CCP4BB list, click the following link:
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