Re: [ccp4bb] Absence of contact between layers in a crystal

There should be two broad types of statistical disorder, short range and long range. The latter for example could consist of two distinct populations of crystal with near identical unit cells so the spots nearly overlap in reciprocal space. If there is a layer structure, shift disorder between

Re: [ccp4bb] Absence of contact between layers in a crystal

On Friday, 06 February, 2015 13:38:14 Rachel Kramer Green wrote: > Dear CCP4BB users, > > For additional information on this matter, please see: > > wwPDB Statement on Retraction of PDB Entries > http://www.wwpdb.org/documentation/UAB.php > > and > > Safeguarding the integrity of protein archiv

Re: [ccp4bb] Absence of contact between layers in a crystal

Dear CCP4BB users, For additional information on this matter, please see: wwPDB Statement on Retraction of PDB Entries http://www.wwpdb.org/documentation/UAB.php and Safeguarding the integrity of protein archive /Nature/ (2010) *463*:425. doi:10.1038/463425c

Re: [ccp4bb] Absence of contact between layers in a crystal

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

Re: [ccp4bb] Absence of contact between layers in a crystal

. Februar 2015 14:08 To: CCP4BB@JISCMAIL.AC.UK 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

Re: [ccp4bb] Absence of contact between layers in a crystal

[ example structures with disordered crystal contacts ] Yes and they all have a good bulk solvent correction. -Bryan

Re: [ccp4bb] Absence of contact between layers in a crystal

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

Re: [ccp4bb] Absence of contact between layers in a crystal

eb 2015, at 11:09, Robbie Joosten wrote: Not in real crystal structures ;) Cheers, Robbie Sent with my Windows Phone Van: Kerff Fred Verzonden: ‎6-‎2-‎2015 12:02 Aan: CCP4BB@JISCMAIL.AC.UK Onderwerp: [ccp4bb] Absence of contact between layers in a crystal Hello, Looking at structure 2HR0 (&qu

Re: [ccp4bb] Absence of contact between layers in a crystal

6-Feb-2015 Dear Adrian Maybe a petition could be circulated that many of us could sign requesting Nature to retract this paper. I don’t know if this has ever been tried, but my guess is that Nature would take it seriously, especially due to the overwhelming evidence that the structure was fabrica

Re: [ccp4bb] Absence of contact between layers in a crystal

Hi Fred, 2015-02-06 11:58 GMT+01:00 Kerff Fred : > 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

Re: [ccp4bb] Absence of contact between layers in a crystal

t; Randy >> >> On 6 Feb 2015, at 11:09, Robbie Joosten wrote: >> >>> Not in real crystal structures ;) >>> >>> Cheers, >>> Robbie >>> >>> Sent with my Windows Phone >>> Van: Kerff Fred >>> Verzonden: ‎6

Re: [ccp4bb] Absence of contact between layers in a crystal

Dave Just for the record, the Wikipedia article you refer to is incorrect in stating that 2HR0 (and possibly others) has been obsoleted: it has not (as others have bemoaned!). Cheers -- Ian On 6 February 2015 at 11:08, David Briggs wrote: > Haven'tthat paper and the associated structure been

Re: [ccp4bb] Absence of contact between layers in a crystal

Well maybe some pressure should be put on Nature to retract the article, so that we can get the publication out of the PDB? It’s not good that it is there for the unwary. Adrian On 06 Feb 2015, at 11:44, Folmer Fredslund wrote: > Unfortunately, the st

Re: [ccp4bb] Absence of contact between layers in a crystal

wrote: > >> Not in real crystal structures ;) >> >> Cheers, >> Robbie >> >> Sent with my Windows Phone >> Van: Kerff Fred >> Verzonden: ‎6-‎2-‎2015 12:02 >> Aan: CCP4BB@JISCMAIL.AC.UK >> Onderwerp: [ccp4bb] Absence of contact betwee

Re: [ccp4bb] Absence of contact between layers in a crystal

Unfortunately, the structure and associated paper for PDB id 2hr0 has _not_ been retracted, or marked as invalid. The University of Alabama had a note about it, but only some of the affected PDB entries were removed. http://www.uab.edu/reporterarchive/71570-uab-statement-on-protein-data-bank-issue

Re: [ccp4bb] Absence of contact between layers in a crystal

@cam.ac.uk Subject: Re: [ccp4bb] Absence of contact between layers in a crystal To: CCP4BB@JISCMAIL.AC.UK 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 a

Re: [ccp4bb] Absence of contact between layers in a crystal

obbie_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

Re: [ccp4bb] Absence of contact between layers in a crystal

why are these structures still in the PDB? On 6 Feb 2015, at 11:08, David Briggs wrote: > Haven'tthat paper and the associated structure been retracted? > > http://www.nature.com/news/2009/091222/full/462970a.html > > There was a huge scandal when it was discovered that Krishna Murthy had > f

Re: [ccp4bb] Absence of contact between layers in a crystal

ten wrote: > Not in real crystal structures ;) > > Cheers, > Robbie > > Sent with my Windows Phone > Van: Kerff Fred > Verzonden: ‎6-‎2-‎2015 12:02 > Aan: CCP4BB@JISCMAIL.AC.UK > Onderwerp: [ccp4bb] Absence of contact between layers in a crystal > > Hello, >

Re: [ccp4bb] Absence of contact between layers in a crystal

This is a famously fabricated crystal structure - the absence of contact was one of the clues, see http://www.nature.com/nature/journal/v448/n7154/full/nature06102.html Cheers, Matt. On 2015-02-06 11:58, Kerff Fred wrote: Hello, Looking at structure 2HR0 ("The structure of complement C3b p

Re: [ccp4bb] Absence of contact between layers in a crystal

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

Re: [ccp4bb] Absence of contact between layers in a crystal

Haven'tthat paper and the associated structure been retracted? http://www.nature.com/news/2009/091222/full/462970a.html There was a huge scandal when it was discovered that Krishna Murthy had falsified data, including the structure you refer to. See http://en.wikipedia.org/wiki/H.M._Krishna_Murt

[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 co