Re: [ccp4bb] Peptide on two-fold axis - was:[ccp4bb] PEG molecule crossing a two-fold crystallographic symmetry axis

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Date: 2009-04-29

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Subject: Re: Peptide on two-fold axis - was: PEG molecule crossing a two-fold crystallographic symmetry axis
From: lidefeng lidefeng {- at -} MOON {- dot -} IBP {- dot -} AC {- dot -} CN
Date: 2009-04-29

Dear Tim Gruene,

But how to illustrate the other one half occupancy of peptide? Disorder ?

Your sincerely
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡De-Feng Li
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡lidefeng@moon.ibp.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2009-04-30

Defeng Li, Dr.,
Email: lidefeng@moon.ibp.ac.cn
National Laboratory of Biomacromolecules,
Institute of Biophysics, Chinese Academy of Sciences,
15 Datun Road, Chaoyang District,
Beijing 100101, China

======= 2009-04-29 10:55:00 You writed in your letter£º=======

>Hello De-Feng Li,
>
>first of all sorry for changing the subject: I think starting a new thread
>from an existing one may hamper people who are going to search the
>archives in the future, therefore it is good practice to give it its
>separate subject line, even though it certainly is be very closely
>related.
>
>In your case you can refine two peptides each with an occupancy of 0.5,
>one for each direction.
>
>Tim
>--
>Tim Gruene
>Institut fuer anorganische Chemie
>Tammannstr. 4
>D-37077 Goettingen
>
>GPG Key ID = A46BEE1A
>
>
>On Wed, 29 Apr 2009, lidefeng wrote:
>
>> Hi everyone,
>>
>> Following Chandrika's question, what should I do if one peptide chain crosses a two-fold crystallographic symmetry axis?
>> The peptide is not symmetric and the sidechain of one Se-Met (two after CS operation) is determined and conformed by MAD.
>>
>> Your sincerely
>> ????????De-Feng Li
>> ????????lidefeng@moon.ibp.ac.cn
>> ??????????2009-04-29
>>
>> Defeng Li, Dr.,
>> Email: lidefeng@moon.ibp.ac.cn
>> National Laboratory of Biomacromolecules,
>> Institute of Biophysics, Chinese Academy of Sciences,
>> 15 Datun Road, Chaoyang District,
>> Beijing 100101, China
>>
>>
>> ======= 2009-04-29 17:02:00 You writed in your letter?=======
>>
>>> Hello everyone,
>>>
>>> My protein crystallised in the spacegroup P6522 with one protein molecule in the asymmetric unit. I have a PEG molecule from the crystallization condition which crosses a two-fold crystallographic symmetry axis. PEG is symmetric hence this does not violate the crystal symmetry. However, this situation causes two problems which I need to solve :
>>>
>>> First, How can I refine this structure ? I am using Phenix. Is there a way to remove van der Waals repulsion between one half occupancy PEG and its crystallographic symmetry mate ?
>>>
>>> Second, how do I submit this structure to PDB ? Do I include a full PEG molecule at half occupancy even though one half is related to the other via crystallographic symmetry ?
>>>
>>> Thanks,
>>> Chandrika
>>
>> ========================================================
>>
>>

========================================================

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: use of siliconized cover glass
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2009-04-29

Next message:
Subject: A post-doctoral position: Drs.H. Moriyama and J. F. Storz at the University of Nebraska.
From: dumpy fly dumpy {- dot -} fly {- at -} GMAIL {- dot -} COM
Date: 2009-04-29