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CCP4BB  December 2008

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Subject:

Re: Refmac and MSE?

From:

Martin Hallberg <[log in to unmask]>

Reply-To:

Martin Hallberg <[log in to unmask]>

Date:

Sat, 20 Dec 2008 09:45:50 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (67 lines)

Hi,
Have you specified the right form factor for Se given
the wavelength used in your experiment?

anomalous formfactor [Name] [f'] [f'']

You can also try the new option where you can do simultaneous
SAD phasing and refinement. See: http://tinyurl.com/8on2cr

You will have to upgrade from your present REFMAC5.2 version to use  
these functions.

Best regards,

Martin

On Dec 20, 2008, at 5:17 AM, Dima Klenchin wrote:

> Hello,
>
> I am at a loss on what's going on:
>
> I am refining SeMET containing structure and using REFMAC 5.2.0005  
> on Linux and, the same thing happening, using REFMAC 5.5.0070 on  
> Windows.
>
> When MET were modelled, there were no difference peaks anywhere.  
> When I changed them all to MSE, the large difference density peaks  
> showed up. So either the protein does not contain SeMet or Refmac  
> somehow uses sulfur scattering factors during refinement.
>
> I have hard time believing the former because 1) the protein was  
> checked by mass spec to be correct size for SeMet derivative, 2) the  
> structure was solved by SAD with all five sites correctly found (196  
> residues total), 3) first 50 aa of the protein are identical to a  
> known structure.
>
> This is 2.4A resolution and at this point R/Rfree = 25/29.
>
> Refmac log shows correct scattering factors read out:
>  SE    17.0006   2.4098   5.8196   0.2726   3.9731  15.2372   4.3543  
> 43.8163   2.8409
>
> The PDB has this for MSE:
> ATOM   1140  N   MSE A 143      35.708 161.163  13.715  1.00  
> 78.82           N
> ATOM   1141  CA  MSE A 143      35.995 162.467  13.106  1.00  
> 77.86           C
> ATOM   1142  CB  MSE A 143      36.307 162.307  11.617  1.00  
> 78.79           C
> ATOM   1143  CG  MSE A 143      37.755 162.127  11.119  1.00  
> 80.89           C
> ATOM   1144 SE   MSE A 143      37.503 161.104   9.363  1.00  
> 91.22          SE
> ATOM   1145  CE  MSE A 143      39.169 160.021   9.696  1.00  
> 86.47           C
> ATOM   1146  C   MSE A 143      34.709 163.226  13.030  1.00  
> 77.70           C
> ATOM   1147  O   MSE A 143      34.682 164.436  12.737  1.00  
> 77.33           O
>
> Any clues greatly appreciated!
>
> Dima
>
>
>

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