We found something similar for a DNA quadruplex not too long ago (4U92).
This had surprisingly high resolution (1.5 Å) for having roughly half of
the ASU being disordered.
On 02/06/2015 06:51 AM, Andrew Leslie 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 <rj...@cam.ac.uk
<mailto:rj...@cam.ac.uk>> 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 <robbie_joos...@hotmail.com
<mailto:robbie_joos...@hotmail.com>> wrote:
Not in real crystal structures ;)
Cheers,
Robbie
Sent with my Windows Phone
------------------------------------------------------------------------
Van: Kerff Fred <mailto:fke...@ulg.ac.be>
Verzonden: 6-2-2015 12:02
Aan: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
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 <t...@shelx.uni-ac.gwdg.de
<mailto:t...@shelx.uni-ac.gwdg.de>> a écrit :
>
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> 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
>
> -----BEGIN PGP SIGNATURE-----
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>
> iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
> j0JFZac4kAh8twpov71MG84=
> =XN57
> -----END PGP SIGNATURE-----
------
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: rj...@cam.ac.uk <mailto:rj...@cam.ac.uk>
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
