Re: [ccp4bb] non-waters among structured solvent atoms
Is there any reason why crystallographers have not routinely substituted NaBr for NaCl in protein crystallization stocks, or even pH'd their TRIS with HBr, if there is no NaCl? Wouldn't it make a lot of sense, since there would always be a possibility for a Br- derivative, and the price difference is pretty small? Also, a data set at the Br- peak would always be able to distinguish heavy H2O from weak halide sites once the structure was solved, even if the sites were not good enough for phase determination themselves. JPK On Wed, Jun 15, 2011 at 7:35 AM, Stephen Graham sc...@cam.ac.uk wrote: You might also want to try: http://www.ncbi.nlm.nih.gov/pubmed?term=12499536 Cheers, Stephen On 15 June 2011 02:09, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Wolfram, This was an early study on the subject: http://www.ncbi.nlm.nih.gov/pubmed/8594192 The software is still accessible via the STAN server. Cheers, Robbie Date: Tue, 14 Jun 2011 17:51:21 -0400 From: wtem...@gmail.com Subject: [ccp4bb] non-waters among structured solvent atoms To: CCP4BB@JISCMAIL.AC.UK Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Many thanks, Wolfram Tempel -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] non-waters among structured solvent atoms
Yes! Although the Rb edge might be a little tricky to get to, but the extra density would probably show up. Also, does Rb substitute well for Na? Rb: Edge keV A K15.19970.8157 I was thinking that perhaps the reason that solvent HAs were not used historically is that perhaps at RT they would induce a lot of secondary radiation damage due to diffusion of radicals, whereas at cryo temperatures that would not be such an issue? Anyway, one would think these substitutions would always be worthwhile, and their power could be greatly enhanced by doing SIRAS against Cl if need be. JPK On Thu, Jun 16, 2011 at 10:22 AM, Edward A. Berry ber...@upstate.edu wrote: Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH? I haven't checked the price. Jacob Keller wrote: Is there any reason why crystallographers have not routinely substituted NaBr for NaCl in protein crystallization stocks, or even pH'd their TRIS with HBr, if there is no NaCl? Wouldn't it make a lot of sense, since there would always be a possibility for a Br- derivative, and the price difference is pretty small? Also, a data set at the Br- peak would always be able to distinguish heavy H2O from weak halide sites once the structure was solved, even if the sites were not good enough for phase determination themselves. JPK On Wed, Jun 15, 2011 at 7:35 AM, Stephen Grahamsc...@cam.ac.uk wrote: You might also want to try: http://www.ncbi.nlm.nih.gov/pubmed?term=12499536 Cheers, Stephen On 15 June 2011 02:09, Robbie Joostenrobbie_joos...@hotmail.com wrote: Hi Wolfram, This was an early study on the subject: http://www.ncbi.nlm.nih.gov/pubmed/8594192 The software is still accessible via the STAN server. Cheers, Robbie Date: Tue, 14 Jun 2011 17:51:21 -0400 From: wtem...@gmail.com Subject: [ccp4bb] non-waters among structured solvent atoms To: CCP4BB@JISCMAIL.AC.UK Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Many thanks, Wolfram Tempel -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] non-waters among structured solvent atoms
Maybe all those highly disordered bromides (and rubidium ions) would be difficult to model and would push up the R factors? From the point of view of SAD or MAD phasing, a large number of partially occupied sites might be difficult to find. The highly disordered sites might also create an anomalous signal at low resolution that would interfere with the signal from the more ordered sites that one would like to use for phasing (we suspect that we may have been thwarted by this in a recent sulfur-SAD experiment that was crystallized from a high NaCl concentration). George On Thu, Jun 16, 2011 at 10:38:41AM -0500, Jacob Keller wrote: Yes! Although the Rb edge might be a little tricky to get to, but the extra density would probably show up. Also, does Rb substitute well for Na? Rb: Edge keV A K15.19970.8157 I was thinking that perhaps the reason that solvent HAs were not used historically is that perhaps at RT they would induce a lot of secondary radiation damage due to diffusion of radicals, whereas at cryo temperatures that would not be such an issue? Anyway, one would think these substitutions would always be worthwhile, and their power could be greatly enhanced by doing SIRAS against Cl if need be. JPK On Thu, Jun 16, 2011 at 10:22 AM, Edward A. Berry ber...@upstate.edu wrote: Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH? I haven't checked the price. Jacob Keller wrote: Is there any reason why crystallographers have not routinely substituted NaBr for NaCl in protein crystallization stocks, or even pH'd their TRIS with HBr, if there is no NaCl? Wouldn't it make a lot of sense, since there would always be a possibility for a Br- derivative, and the price difference is pretty small? Also, a data set at the Br- peak would always be able to distinguish heavy H2O from weak halide sites once the structure was solved, even if the sites were not good enough for phase determination themselves. JPK On Wed, Jun 15, 2011 at 7:35 AM, Stephen Grahamsc...@cam.ac.uk wrote: You might also want to try: http://www.ncbi.nlm.nih.gov/pubmed?term=12499536 Cheers, Stephen On 15 June 2011 02:09, Robbie Joostenrobbie_joos...@hotmail.com wrote: Hi Wolfram, This was an early study on the subject: http://www.ncbi.nlm.nih.gov/pubmed/8594192 The software is still accessible via the STAN server. Cheers, Robbie Date: Tue, 14 Jun 2011 17:51:21 -0400 From: wtem...@gmail.com Subject: [ccp4bb] non-waters among structured solvent atoms To: CCP4BB@JISCMAIL.AC.UK Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Many thanks, Wolfram Tempel -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638 -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] non-waters among structured solvent atoms
Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH? I haven't checked the price. Including shipping in the US RbBr: 50 g 99% pure is ~$150. RbOH: 25g 99+% pure in 50 % water runs about ~$120. It would be interesting to see how the substitution would influence the crystallization or crystal integrity such as a quick soak just before data collection. Hope that helps, Sean P212121 http://store.p212121.com/
Re: [ccp4bb] non-waters among structured solvent atoms
Sean Seaver wrote: Better yet, RbBr? and pH MES, MOPS, and HEPES with RbOH? I haven't checked the price. Including shipping in the US RbBr: 50 g 99% pure is ~$150. RbOH: 25g 99+% pure in 50 % water runs about ~$120. It would be interesting to see how the substitution would influence the crystallization or crystal integrity such as a quick soak just before data collection. I seem to remember that Br(-) at high concentrations is pretty chaotropic. Something about NaBr wash to remove peripheral protein from membranes. eab
Re: [ccp4bb] non-waters among structured solvent atoms
You might also want to try: http://www.ncbi.nlm.nih.gov/pubmed?term=12499536 Cheers, Stephen On 15 June 2011 02:09, Robbie Joosten robbie_joos...@hotmail.com wrote: Hi Wolfram, This was an early study on the subject: http://www.ncbi.nlm.nih.gov/pubmed/8594192 The software is still accessible via the STAN server. Cheers, Robbie Date: Tue, 14 Jun 2011 17:51:21 -0400 From: wtem...@gmail.com Subject: [ccp4bb] non-waters among structured solvent atoms To: CCP4BB@JISCMAIL.AC.UK Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Many thanks, Wolfram Tempel -- Dr Stephen Graham 1851 Research Fellow Cambridge Institute for Medical Research Wellcome Trust/MRC Building Addenbrooke's Hospital, Hills Road Cambridge, CB2 0XY, UK Phone: +44 1223 762 638
Re: [ccp4bb] non-waters among structured solvent atoms
On Tue, Jun 14, 2011 at 2:51 PM, wtempel wtem...@gmail.com wrote: Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Do you mean metals incorrectly annotated as waters, or vice-versa? The latter case is discussed here: http://www.ncbi.nlm.nih.gov/pubmed/18614239 -Nat
Re: [ccp4bb] non-waters among structured solvent atoms
How about halides? Anyone know of criteria for their binding sites? JPK ps Funny how my recent post was about almost exactly the same thing--serendipity, I guess? On Tue, Jun 14, 2011 at 5:07 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Tue, Jun 14, 2011 at 2:51 PM, wtempel wtem...@gmail.com wrote: Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Do you mean metals incorrectly annotated as waters, or vice-versa? The latter case is discussed here: http://www.ncbi.nlm.nih.gov/pubmed/18614239 -Nat -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] non-waters among structured solvent atoms
A coordination distance table (metals, Cl) is in Marjorie Harding's papers 1. Harding M (2006) Small revisions to predicted distances around metal sites in proteins. Acta Crystallogr. D62(6), 678-682. 2. Harding M (2004) The architecture of metal coordination groups in proteins. Acta Crystallogr. D60(5), 849-859. and my (book)appendix. For anions see various Weiss, Dauter, Cie soaking papers A figure of a typical Cl which often mask/pass as 'heavy' waters (improbably low B) around 3.2 A coord dist here: http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp hy_Fig_12-42.htm BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller Sent: Tuesday, June 14, 2011 4:27 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] non-waters among structured solvent atoms How about halides? Anyone know of criteria for their binding sites? JPK ps Funny how my recent post was about almost exactly the same thing--serendipity, I guess? On Tue, Jun 14, 2011 at 5:07 PM, Nat Echols nathaniel.ech...@gmail.com wrote: On Tue, Jun 14, 2011 at 2:51 PM, wtempel wtem...@gmail.com wrote: Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Do you mean metals incorrectly annotated as waters, or vice-versa? The latter case is discussed here: http://www.ncbi.nlm.nih.gov/pubmed/18614239 -Nat -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] non-waters among structured solvent atoms
Hi Wolfram, This was an early study on the subject: http://www.ncbi.nlm.nih.gov/pubmed/8594192 The software is still accessible via the STAN server. Cheers, Robbie Date: Tue, 14 Jun 2011 17:51:21 -0400 From: wtem...@gmail.com Subject: [ccp4bb] non-waters among structured solvent atoms To: CCP4BB@JISCMAIL.AC.UK Dear colleagues, following a discussion in our lab, I have volunteered to dig out articles from the literature about erroneous assignments of non-water entities such as metal ions, halides in protein models. For example I have the faint recollection that data mining of the PDB for suspect water assemblies matching the geometry of coordinated cations has previously been described. But none of my google searches has turned up the references I was looking for. Could someone point me in the right direction, please? Many thanks, Wolfram Tempel
