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Re: [ccp4bb] How to improve the density of another molecule in Asymmetric unit
 

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CCP4bb <-- 2008 <-- January 2008 <-- 16 January 2008
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Subject: postdoc position in structural biology of wound healing
From: David Hulmes d {- dot -} hulmes {- at -} IBCP {- dot -} FR
Date: 2008-01-16 		Next message:
Subject: Re: How to improve the density of another molecule in Asymmetric unit
From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-16


Subject: Re: How to improve the density of another molecule in Asymmetric unit
From: Gerard DVD Kleywegt gerard {- at -} XRAY {- dot -} BMC {- dot -} UU {- dot -} SE
Date: 2008-01-16
ni hao,

> I have a question about how to improve the electron density. I have two
> indepedent molecules in the asymmetric unit (1.9 A resolution). I solved the
> structure with PHASER and refined with CCP4i (Rfree = 0.29).
>
> For the first molecule, the density is very good, but for the second one,
> the density is much worse than the first one. Are there any ways to improve
> the density of the second molecule, such as some kinds of averaging? Why
> that happens?

there can be various causes for this such as undetected twinning or a
spacegroup error. if you can exclude those possibilities, it could also be
that the weak-density molecule has fewer packing interactions and thus is less
well ordered, and therefore has a higher overall temperature factor. you can
investigate this with SPANCSI (http://xray.bmc.uu.se/usf/spancsi_man.html#H5).

--dvd

******************************************************************
Gerard J. Kleywegt
[Research Fellow of the Royal Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN

http://xray.bmc.uu.se/gerard/ mailto:gerard@xray.bmc.uu.se
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CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 16 January 2008
Previous message:
Subject: postdoc position in structural biology of wound healing
From: David Hulmes d {- dot -} hulmes {- at -} IBCP {- dot -} FR
Date: 2008-01-16 		Next message:
Subject: Re: How to improve the density of another molecule in Asymmetric unit
From: Lijun Liu liulj {- at -} UOXRAY {- dot -} UOREGON {- dot -} EDU
Date: 2008-01-16


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