Hi,
With this resolution and R-factors, I would guess you are not missing that much
– certainly not large bits of DNA. Do you have Phosphate or Sulphate in the
crystallisation buffer? If so, you may just be seeing Phosphate/Sulphate where
the DNA would bind.
Cheers,
Mark
Dr S.M. Roe,
X-Ray Facility Manager,
Tel. (+44) 01273 678863 (Office)
School of Life Sciences,
Tel. (+44) 01273 872896 (X-Ray Lab)
University of Sussex,
Tel. (+44) 0782 5501579 (Mobile)
Falmer,
East Sussex.
E-mail
m....@sussex.ac.uk<mailto:m....@sussex.ac.uk>
BN1 9RQ
Web
http://www.sussex.ac.uk/lifesci/roelab/
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Meiting Yang
<meitingyang1...@163.com>
Reply to: Meiting Yang <meitingyang1...@163.com>
Date: Friday, 17 December 2021 at 08:04
To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] the complex structure of protein and DNA
Dear Petr,
Thank you very much for your reply!
The complex structure was refined finally to 2.44 Å resolution with an Rwork of
23.7% and an Rfree of 27.4%.
We didn't try automatic DNA building tools, I don't know much about this. Thank
you very much for your advice, I'm going to study it.
Could you please give some specific suggestions about automatic DNA building
tools?
Thank you very much.
At 2021-12-17 15:01:44, "Petr Kolenko" <petr.kole...@fjfi.cvut.cz> wrote:
>Dear Yang Meiting,
>There are few things to know better about your structures first:
>1) What is the resolution of the complex structure?
>2) In what stage of structure refinement you are? Rwork/free would help.
>3) Have you tried some automatic DNA building tools?
>I am not surprised that you can see only a fraction of DNA.I guess, solvent
>flattening may also decrease the visibility of this region. The only thing I
>would suggest now, do not expect to see the whole DNA immediately. Just start
>with the step-wise building if possible. The rest may appear in the later
>stage of model building.
>Best regards,
>Petr
>________________________________________
>From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Meiting Yang
><meitingyang1...@163.com>
>Sent: Friday, December 17, 2021 7:29:54 AM
>To: CCP4BB@JISCMAIL.AC.UK
>Subject: [ccp4bb] the complex structure of protein and DNA
>
>Dear all，
>We have determined two Crystal structures, with one is apo structure and the
>other is a complex of the same protein with double-stranded DNA. In the
>complex, the protein structure is clearly viible, but the DNA only can be seen
>several phosphate groups. We want to know how do we get the complete DNA
>structure.
>The space group of the apo structure is P222, one asymmetric unit including
>two protein molecules. The space group of the complex structure is P2, one
>unit containing two protein molecules, 5 phosphate groups just situated near
>one protein molecules. The binding ability of the DNA and the protein is about
>1 μM. The DNA we used for crystallization is 18 bp double-stranded DNA, but
>now only 5 phosphate groups can be observed. The crystal we have identified is
>a complex rather than a monomer, the cell parameters of complexes and monomers
>are different.
>Here, we want to get some suggestions, to get the complexe that contain the
>entire DNA structure.
>Best regards.
>
>
>
>
>
>
>________________________________
>
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