In our structures 1H6W (1.9Å) and 1OCY (1.5Å) we observed something similar, I
suspect the domain that makes the crystal contacts is three-fold disordered,
leading to layers of nothing. In our paper in JMB 314, 1137 (doi
10.1006/jmbi.2000.5204) we tried to explain it a bit, and describe what was
done to try and "show up" the missing domain.
The 2HR0 structure was clearly made up, as were the data, apparently the
mathematical function used to calculate the sigmas could be derived from the
deposited data...It is indeed a pity that neither the structure nor the paper
have been rejected. Perhaps the PDB is waiting for Nature, and Nature for the
PDB...a joint letter to both might be in order to get this sorted out.
On 6 Feb 2015, at 11:58, Kerff Fred wrote:
> 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-----
Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij
