Hi Chen,
I see your point now. Yes, I agree that the 80:20 method (or 75:25 as stated
in the paper, [log in to unmask]" target="_blank">http:[log in to unmask]) is
a very useful technique. The fact that it does not take much effort or lead
to uncertainties makes it very worth trying.
Here I add my two cents: when performing such optimizations, try both
seeding and no-seeding if quantity of protein permits. If protein quantity
is limited and the crystals are reluctant to appear under the original
condition, then seeding is always a good idea.
Zhijie
--------------------------------------------------
From: "chen c" <[log in to unmask]>
Sent: Sunday, April 29, 2012 6:09 PM
To: "Zhijie Li" <[log in to unmask]>
Subject: Re: [ccp4bb] Anisotropic diffraction
> I accept your advice. In fact, this is the first time I am involved in
> anisotropic issue. And I learned a lot from all the above discussion.
>
> However, the 80:20 optimization method(an example of "long-tail
> theory") rather than surface mutation is what I want to emphasis in my
> last email. As illustrated in the attached pdf, it defenitely deserve
> a try. One more thing to mention is that this very 80:20 method can be
> very versatile and useful in optimising macromolecular crystals in
> case of issues more than anistropic problem.
>
> best regards
> chen
>
>
>
> 2012/4/30 Zhijie Li <[log in to unmask]>:
>> Hi Chen,
>>
>> It is a reality that a usable protein dataset could take years of hard
>> work
>> to obtain. Compared to problems such as twining, bad diffraction
>> patterns,
>> excessive mosaicity, low resolution, weak, noisy anomalous signal, etc.,
>> anisotropic diffraction should probably be regarded most benign. There is
>> nothing wrong with publishing a properly treated anisotropic dataset.
>> Then
>> why risking another year trying to find a better mutant? There is no
>> guarantee that the mutants would work better, or even work.
>>
>> Unless the crystal is naturally isotropic, such as that it is in a cubic
>> space group, the diffraction of protein crystals will probably always be
>> more or less anisotropic. This only reflects the fact that the crystal
>> packing is indeed anisotropic, consequently the movements of the Unit
>> cell
>> is anisotropic. It does not mean that there would be defects in the
>> resulting structure. For instance, a 3A isotropic dataset, and a 2.5-2A
>> anisotropic dataset, which one is going to give a better description of
>> the
>> protein?
>>
>> Zhijie
>>
>>
>> --------------------------------------------------
>> From: "chen c" <[log in to unmask]>
>> Sent: Sunday, April 29, 2012 5:03 AM
>> To: "Zhijie Li" <[log in to unmask]>
>>
>> Subject: Re: [ccp4bb] Anisotropic diffraction
>>
>>> If we might be able to eliminate the anisotropic diffraction issue,
>>> which might mean and reflect defect in structure. Why not just
>>> restrain our thought to solve this question by data processing, etc?
>>>
>>> chen
>>>
>>> 2012/4/28 Zhijie Li <[log in to unmask]>:
>>>>
>>>> Hi Cheng,
>>>>
>>>> This paper looks quite irrelevant to Theresa's question.
>>>>
>>>> Zhijie
>>>>
>>>>
>>>>
>>>> --------------------------------------------------
>>>> From: "chen c" <[log in to unmask]>
>>>> Sent: Friday, April 27, 2012 10:28 PM
>>>> To: <[log in to unmask]>
>>>> Subject: Re: [ccp4bb] Anisotropic diffraction
>>>>
>>>>
>>>>> Birtley and Curry used a novel optimization method, in their paper
>>>>> "Crystallization of foot-and-mouth disease virus 3C protease: surface
>>>>> mutagenesis and a novel crystal-optimization strategy", which might be
>>>>> inspiring for you.
>>>>>
>>>>>
>>>>>
>>>>> 在 2012年4月28日 上午3:21,David Schuller <[log in to unmask]> 写道:
>>>>>>
>>>>>>
>>>>>> Anisotropic truncation should have no effect on the space group
>>>>>> symmetry.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 04/27/12 15:18, Theresa Hsu wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Dear crystallographers
>>>>>>>
>>>>>>> A very basic question, for anisotropic diffraction, does data
>>>>>>> truncation
>>>>>>> with ellipsoidal method change the symmetry? For example, if
>>>>>>> untruncated
>>>>>>> data is space group P6, will truncated data index as P622 or P2?
>>>>>>>
>>>>>>> Thank you.
>>>>>>>
>>>>>>> Theresa
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> =======================================================================
>>>>>> All Things Serve the Beam
>>>>>> =======================================================================
>>>>>> David J. Schuller
>>>>>> modern man in a post-modern world
>>>>>> MacCHESS, Cornell University
>>>>>> [log in to unmask]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Cheng Chen, Ph.D. Candidate
>>>>> Laboratory of Structural Biology
>>>>> Life Science Building,Tsinghua University
>>>>> Beijing 100084
>>>>> China
>>>>> Tel:+86-10-62772291
>>>>> Fax:+86-10-62773145
>>>>> E-mail:[log in to unmask]
>>>>>
>>>>> 北京市海淀区清华大学生命科学馆201-212室
>>>>> 邮编:100084
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Cheng Chen, Ph.D. Candidate
>>> Laboratory of Structural Biology
>>> Life Science Building,Tsinghua University
>>> Beijing 100084
>>> China
>>> Tel:+86-10-62772291
>>> Fax:+86-10-62773145
>>> E-mail:[log in to unmask]
>>>
>>> 北京市海淀区清华大学生命科学馆201-212室
>>> 邮编:100084
>>
>>
>
>
>
> --
> Cheng Chen, Ph.D. Candidate
> Laboratory of Structural Biology
> Life Science Building,Tsinghua University
> Beijing 100084
> China
> Tel:+86-10-62772291
> Fax:+86-10-62773145
> E-mail:[log in to unmask]
>
> 北京市海淀区清华大学生命科学馆201-212室
> 邮编:100084
>
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