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 layers could occur. These cases should be distinguishable by an examination of the diffraction patterns (probably a bit late for 2ts1). Streaks in certain directions could occur or broader diffuse features. Also perhaps anisotropic resolution. If two populations of crystal, perhaps the spots would be slightly split (in x,y or phi). Main point is if proposing disorder, there should be consequences which could be tested. Whether it is worthwhile to do so is of course another issue. Colin --- 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.ukmailto: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.commailto:robbie_joos...@hotmail.com wrote: -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
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 http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Sincerely, Rachel Green Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu *New!*Deposit X-ray data with the wwPDB at: http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon). ___ Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 2/6/2015 7:35 AM, Mark van Raaij wrote: 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 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- 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 http://www.cnb.csic.es/%7Emjvanraaij
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 archive /Nature/ (2010) *463*:425. doi:10.1038/463425c http://www.nature.com/nature/journal/v463/n7280/full/463425c.html Sincerely, Rachel Green Both of those statements are now 5 years out of date. The linked URLs at UAB are now dead. The link to the US Office of Research Integrity works, but the index to case summaries on that site has no listing for the Murthy affair either as a closed or an open case investigation. Furthermore the promised actions (retraction, obsolesence) apparently never took place for whatever reason. Can you provide an update? Do you think that an open letter from the community would be helpful? Ethan On 2/6/2015 7:35 AM, Mark van Raaij wrote: 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 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- 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 http://www.cnb.csic.es/%7Emjvanraaij -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
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_Murthy A crystallographer with a wikipedia entry for all the wrong reasons... Dave On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be 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 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- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi j0JFZac4kAh8twpov71MG84= =XN57 -END PGP SIGNATURE-
Re: [ccp4bb] Absence of contact between layers in a crystal
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 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 (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 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 RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Absence of contact between layers in a crystal
Not in real crystal structures ;) Cheers, Robbie Sent with my Windows Phone Van: Kerff Fredmailto:fke...@ulg.ac.be Verzonden: 6-2-2015 12:02 Aan: CCP4BB@JISCMAIL.AC.UKmailto: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 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-
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 drdavidcbri...@gmail.com 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 falsified data, including the structure you refer to. See http://en.wikipedia.org/wiki/H.M._Krishna_Murthy A crystallographer with a wikipedia entry for all the wrong reasons... Dave On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be 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 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- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi j0JFZac4kAh8twpov71MG84= =XN57 -END PGP SIGNATURE-
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-issues For 2hr0, the Nature letter ( http://www.nature.com/nature/journal/v444/n7116/full/nature05258.html) and the associated structure has not been removed from the archives. Best regards, Folmer Fredslund Disclosure: I published the structure of native bovine C3 (2b39) 2015-02-06 12:08 GMT+01:00 David Briggs drdavidcbri...@gmail.com: 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_Murthy A crystallographer with a wikipedia entry for all the wrong reasons... Dave On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be 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 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- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi j0JFZac4kAh8twpov71MG84= =XN57 -END PGP SIGNATURE- -- Folmer Fredslund
Re: [ccp4bb] Absence of contact between layers in a crystal
Hi Randy, Indeed, true cases exist. I guess my shock that Nature still didn't retract the paper and as a result of this the PDB didn't obsolete 2hr0 got the better of me. This is not how science is supposed to work. Cheers,Robbie Date: Fri, 6 Feb 2015 11:16:48 + From: rj...@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 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 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 (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 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. ReadDepartment of Haematology, University of CambridgeCambridge Institute for Medical Research Tel: + 44 1223 336500Wellcome Trust/MRC Building Fax: + 44 1223 336827Hills Road E-mail: rj...@cam.ac.ukCambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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 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 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- -- Matthew Bowler Synchrotron Diffraction Group European Molecular Biology Laboratory 71, avenue des Martyrs CS 90181 F-38042 GRENOBLE Cedex 9 FRANCE France === Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.88.29.04 http://www.embl.fr/ ===
Re: [ccp4bb] Absence of contact between layers in a crystal
Thanks for all the replies and sorry for rerun of a thread. I however have two additional questions: - Why is the pdb still available without any obvious sign of the fraud? - Why is the paper stil available ? 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 12:16, Randy Read rj...@cam.ac.uk a écrit : 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- 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 RoadE-mail: rj...@cam.ac.uk mailto:rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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 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 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- 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
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 drdavidcbri...@gmail.com 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 falsified data, including the structure you refer to. See http://en.wikipedia.org/wiki/H.M._Krishna_Murthy A crystallographer with a wikipedia entry for all the wrong reasons... Dave On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be 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 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- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi j0JFZac4kAh8twpov71MG84= =XN57 -END PGP SIGNATURE-
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
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 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 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 (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 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 RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Absence of contact between layers in a crystal
Hi Fred, 2015-02-06 11:58 GMT+01:00 Kerff Fred fke...@ulg.ac.be: 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? Come to think of it, in the communication ( http://www.nature.com/nature/journal/v448/n7154/full/nature06103.html) Ajees et al., mention that they actually don't have gaps, but just some low occupancy contaminant that makes crystal contacts. So, even with this structure being fraud, you would not be able to use it as an example of absence of crystal contacts. Best regards, Folmer Fredslund 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 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- -- Folmer Fredslund
Re: [ccp4bb] Absence of contact between layers in a crystal
Hi, Another example is 2ZW3, again a membrane protein. Best regards, Takanori Nakane On 2015/02/06 21:11, Adrian Goldman wrote: 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 and...@mrc-lmb.cam.ac.uk 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 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 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 (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 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 RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Absence of contact between layers in a crystal
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 and...@mrc-lmb.cam.ac.uk 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 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 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 (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 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 RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk signature.asc Description: Message signed with OpenPGP using GPGMail
Re: [ccp4bb] Absence of contact between layers in a crystal
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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Paukstelis Sent: Freitag, 6. 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 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 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 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 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 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 RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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 folm...@gmail.com wrote: 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-issues For 2hr0, the Nature letter ( http://www.nature.com/nature/journal/v444/n7116/full/nature05258.html) and the associated structure has not been removed from the archives. Best regards, Folmer Fredslund Disclosure: I published the structure of native bovine C3 (2b39) 2015-02-06 12:08 GMT+01:00 David Briggs drdavidcbri...@gmail.com: 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_Murthy A crystallographer with a wikipedia entry for all the wrong reasons... Dave On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be 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 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- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi j0JFZac4kAh8twpov71MG84= =XN57 -END PGP SIGNATURE- -- Folmer Fredslund signature.asc Description: Message signed with OpenPGP using GPGMail
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 fabricated. Adrian, would you possibly consider drafting a short msg, with a pointer to a file (maybe in the ccp4 archives) with the evidence, that could serve as the the basis of a petition to Nature??? best regards, Joel On 6Feb, 2015, at 14:01, Adrian Goldman adrian.gold...@helsinki.fi wrote: 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 folm...@gmail.com wrote: 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-issues For 2hr0, the Nature letter ( http://www.nature.com/nature/journal/v444/n7116/full/nature05258.html) and the associated structure has not been removed from the archives. Best regards, Folmer Fredslund Disclosure: I published the structure of native bovine C3 (2b39) 2015-02-06 12:08 GMT+01:00 David Briggs drdavidcbri...@gmail.com: 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_Murthy A crystallographer with a wikipedia entry for all the wrong reasons... Dave On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be 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 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- Version: GnuPG v1.4.12 (GNU/Linux) iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi j0JFZac4kAh8twpov71MG84= =XN57 -END PGP SIGNATURE- -- Folmer Fredslund
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 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- 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: rj...@cam.ac.uk mailto:rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
