Hi,
Another example is 2ZW3, again a membrane protein.
Best regards,
Takanori Nakane
On 2015/02/06 21:11, Adrian Goldman wrote:
Our recent membrane protein structure (4av3) doesn’t have much in the way of
contacts either, as is characteristic of type 1 membrane protein crystals.
Adrian
On 06 Feb 2015, at 11:51, Andrew Leslie <[email protected]> wrote:
Just to give a concrete example of Randy's point, PDB entry 2ts1 for tyrosyl tRNA
synthetase has "layers" of molecules with no contact between the layers. This
is because the domain (residues 320-419) that was providing the contacts in this
direction was disordered and could not be modelled (there was very little density in this
region). It is perhaps surprising that in spite of the disorder the crystals diffracted
very well (2.3Å data collected on film).
Andrew
On 6 Feb 2015, at 11:16, Randy Read <[email protected]> wrote:
Actually, if you go back through the archive of CCP4-BB from the first time
this came up, I think you'll find that there are real crystals with apparent
gaps in the packing. This can arise because of statistical disorder, where
there are two or more ways that a statistically-disordered layer in the crystal
can mediate the interaction between ordered layers. So not finding a connected
packing is something to look closely at and worry about, but it doesn't
necessarily indicate that somebody did a bad job of making up a structure.
Randy
On 6 Feb 2015, at 11:09, Robbie Joosten <[email protected]> wrote:
Not in real crystal structures ;)
Cheers,
Robbie
Sent with my Windows Phone
Van: Kerff Fred
Verzonden: 6-2-2015 12:02
Aan: [email protected]
Onderwerp: [ccp4bb] Absence of contact between layers in a crystal
Hello,
Looking at structure 2HR0 ("The structure of complement C3b provides insights
into complement activation and regulation. »,Abdul Ajees, A., Gunasekaran, K.,
Volanakis, J.E., Narayana, S.V., Kotwal, G.J., Krishna Murthy, H.M.; (2006)
Nature 444: 221-225), I noticed the absence of contacts between layers in the
crystal. Is it something that has already been observed in other crystals?
Best regards,
Fred
-----
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000 Liège (Belgium)
Tel.: +32 (0)4 3663620
Fax: +32 (0)4 3663772
Le 6 févr. 2015 à 10:12, Tim Gruene <[email protected]> a écrit :
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Dear Smith,
The sca file most likely does not contain flags. pointless can read
the sca file, standardise it to ccp4 standards and freerflag marks
random reflections. You should use the maximum of 500 unique
reflections or 5% of the unique reflections, whichever is larger.
Best,
Tim
On 02/06/2015 09:49 AM, Smith Lee wrote:
Dear All, I have a sca file. Will you please tell me by which
software or how I can know whether the sca file contains R-free
tags? If not, by which software or how I can add the R-free tags?
And how much of the reflections I add the R-free tags? I am looking
forward to getting your reply. Smith
- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [email protected]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
