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Re: [ccp4bb] Li ion scattering factor
 

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CCP4bb <-- 2007 <-- September 2007 <-- 04 September 2007
Previous message:
Subject: Li ion scattering factor
From: Mark Mayer mayerm {- at -} MAIL {- dot -} NIH {- dot -} GOV
Date: 2007-09-04 		Next message:
Subject: Re: Rfree and unaccounted density
From: Ranvir Singh rsvatsa {- at -} YAHOO {- dot -} COM
Date: 2007-09-05


Subject: Re: Li ion scattering factor
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-04
Number of electrons are rarely (if ever) used. In principle sum of
the coefficients of gaussians should be equal to the number of
electrons.

Ions from nonions are distinguished by just addition charge on the
element column. Example:

ATOM 4175 CL CL I 1 5.299 23.521 60.812 1.00
18.77 CL
ATOM 4175 CL CL I 1 5.299 23.521 60.812 1.00
18.77 CL-1
ATOM 3854 O THR B 220 -16.228 28.954 11.993 1.00
7.54 O


Garib

On 4 Sep 2007, at 23:54, Mark Mayer wrote:

> Dear All,
>
> We have a structure under refinement with a putative Li bound to a
> potentially important
> allosteric site. I'd assumed that Li+ would lose an electron and
> have weaker scattering
> than Li Metal, but the entry for atomsf.lib has the same # of
> electrons for both entries
> while the entries for F and F-, Na and Na+ etc all differ by ±1 as
> expected. Since
> the coefficients for the scattering factor calculation are
> different for Li and Li+,
> I guess four crystallographic calculations that's all that matters?
>
> Li
> 3 3 0.037700
> 1.128200 0.750800 0.617500 0.465300
> 3.954600 1.052400 85.390503 168.261002
> 0.001000 0.000000 0.000000 0.000000
> Li+1
> 3 3 0.016700
> 0.696800 0.788800 0.341400 0.156300
> 4.623700 1.955700 0.631600 10.095300
> 0.001000 0.000000 0.000000 0.000000
>
> I also have a general question about how ions are differentiated
> from the unionized atomic species
> in the PDB. Is the left shift by 1 character in column 3 and the
> last column, using Cl as an example
> below, how the PDB (and Refmac) distinguish Cl-1 from Cl?
>
> ATOM 4175 CL CL I 1 5.299 23.521 60.812 1.00
> 18.77 CL
> ATOM 3854 O THR B 220 -16.228 28.954 11.993 1.00
> 7.54 O
>
> Thanks for your input - Mark
>
>

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CCP4bb <-- 2007 <-- September 2007 <-- 04 September 2007
Previous message:
Subject: Li ion scattering factor
From: Mark Mayer mayerm {- at -} MAIL {- dot -} NIH {- dot -} GOV
Date: 2007-09-04 		Next message:
Subject: Re: Rfree and unaccounted density
From: Ranvir Singh rsvatsa {- at -} YAHOO {- dot -} COM
Date: 2007-09-05


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