Follow up on Mark's comment. Both Met and Se-Met structures need to be deposited if you solve the initial structure with Se-Met then attain a better dataset with native Met and use the Se-Met structure for a molecular replacement model. The community should know where the initial structure came from. It's not sufficient to have an MR model appear out of nowhere.
Best wishes,
Reza
Reza Khayat, PhD
Assistant Professor
Department of Chemistry
City College of New York
New York, NY 10031
http://www.khayatlab.org/
212-650-6070
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Mark J van Raaij
Sent: Friday, April 10, 2015 9:43 AM
To: [log in to unmask]
Subject: Re: [ccp4bb] on Se-MET
depends which data you used to refine the final structure.
if your structure is refined against native data, you have to put normal Mets; if it is refined against data collected from a SeMet-containing crystal, SeMets.
I usually deposit both, unless the SeMet structure is much lower resolution than the native.
Of course, there are cases where there is no native, and crystales were obtained only for SeMet-containing protein (perhaps the native was never even tried)
Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
On 10 Apr 2015, at 15:32, Smith Liu wrote:
> Dear All,
>
> I have checked some RCSB deposited PDB files, in the coordinates parts it have the coordinates of the atoms of Se-Met rather than Met. Will you please let me know if we solved the crystal 3-D by Se-Met for phase issue, shoud we deposit the PDB in RCSB with coordinatates for Se-Met or Met?
>
> I am looking forward to getting your reply.
>
> Smith
>
>
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