[ccp4bb] Li ion scattering factor

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CCP4bb <-- 2007 <-- September 2007 <-- 04 September 2007

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Subject: Re: covalently bonded Ligand fit
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-04

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Subject: Re: Li ion scattering factor
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-04

Subject: Li ion scattering factor
From: Mark Mayer mayerm {- at -} MAIL {- dot -} NIH {- dot -} GOV
Date: 2007-09-04

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: Re: covalently bonded Ligand fit
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-04

Next message:
Subject: Re: Li ion scattering factor
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2007-09-04