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 :
>>>>
>>>> -----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-----
>>>> Version: GnuPG v1.4.12 (GNU/Linux)
>>>>
>>>> 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: [email protected]
>> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>>
>
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