One wonders if some of this structures might be good model cases for testing issues like mask intrusion, missing Fpart regions, etc in order to improve bulk solvent corrections….
Best, BR From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Paul Paukstelis Sent: Freitag, 6. Februar 2015 14:08 To: [email protected] Subject: Re: [ccp4bb] Absence of contact between layers in a crystal 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 <[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 <mailto:[email protected]> 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
