Re: [ccp4bb] partial density

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Questions about cryoprotectants
From: Yuan Cheng ycheng {- at -} EMAIL {- dot -} UNC {- dot -} EDU
Date: 2009-10-07

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From: Graeme Winter graeme {- dot -} winter {- at -} GOOGLEMAIL {- dot -} COM
Date: 2009-10-08

Subject: Re: partial density
From: Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM Herman {- dot -} Schreuder {- at -} SANOFI-AVENTIS {- dot -} COM
Date: 2009-10-08

Dear Kumar,
This is perfectly normal. Long and flexible side chains e.g. lysines,
facing the solvent move around and have weak electron density. In fact,
I have not seen a structure where this is not the case. If you get
strong Fo-Fc density back, I would fit the side chains and not worry
about the electron density being below 1 sigma.

best regards,
Herman

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Putcha, Balananda Dhurjati Kumar
Sent: Wednesday, October 07, 2009 6:58 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] partial density

Dear all,
I have refined a structure where several sidechains have only
partial
2Fo-Fc density ( 1 X sigma). I see strong Fo-Fc density in both
omit maps and
when I delete the sidechains, suggesting the presence of the
sidechain.
However, the density is never complete and sometimes only covers
the C-beta
atoms. The structure is at 2.9A and the Rfree is approximately
25% using
BUSTER-TNT (29% with Refmac). I am not sure how to interpret
this and was
wondering if it suggested a disordered or dynamic structure. Are
there any
reports of such structures in the literature?
Thank you
Kumar

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Questions about cryoprotectants
From: Yuan Cheng ycheng {- at -} EMAIL {- dot -} UNC {- dot -} EDU
Date: 2009-10-07

Next message:
Subject: Re: xds and cell refinement in cP
From: Graeme Winter graeme {- dot -} winter {- at -} GOOGLEMAIL {- dot -} COM
Date: 2009-10-08