Hi! As suggested below sulfur/phosphorous anomalous difference Fourier density would be nice, but you might be able to figure out what's going without collecting more data. Have you investigated the direct interaction partners of your mystery oxyanion? Unless you are at extreme pH values, phosphate will have at least one proton that is looking for a hydrogen bond acceptor. In contrast, sulfate/sulphate will generally not have a proton to donate (SO4--). You might want to inspect the binding sites of sulfate and phosphate binding protein, respectively.
My two Kronas, Hudel Date: Sat, 16 Feb 2019 17:05:17 +0800 From: 张士军 <21620150150...@stu.xmu.edu.cn> Subject: SO4 or PO4 Dear all I have got a crystal grown at the condition both have ion of SO4 and PO4, and the diffraction resolution is very well, but the problem is coming: how to tell which is which just from electron density? I think they are exactly same. Thanks a lot !!! Beat Regards Shijun ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Db&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=OEjgsl673YFidwgUiOEydfEtM3rOJN3YPCzIYVvHLJc&e= ------------------------------ Date: Sat, 16 Feb 2019 11:14:07 -0500 From: jlliu20022002 liu <jlliu20022...@gmail.com> Subject: Re: SO4 or PO4 How about collect data at sulfur peak. You might see anomalous peak for sulfur. Jinyu On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn> wrote: > Dear all > > I have got a crystal grown at the condition both have ion of SO4 and PO4, > and the diffraction resolution is very well, but the problem is coming: how > to tell which is which just from electron density? I think they are exactly > same. Thanks a lot !!! > > Beat Regards > > Shijun > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= ------------------------------ Date: Sat, 16 Feb 2019 11:47:55 -0500 From: Roger Rowlett <rrowl...@colgate.edu> Subject: Re: SO4 or PO4 Two things to look at that could provide a clue: Examine the anomalous map for some density over the central atom. Sulfur will often, but not always have significant anomalous density depending on the wavelength and quality of data set. Phosphate is normally HPO4= or H2PO4-. Look for phosphate donor to acceptor hydrogen bonding contacts. Sulfate rarely has donor to acceptor hydrogen bonding contacts, as it is SO4= at any reasonable pH. Roger Rowlett On Sat, Feb 16, 2019, 4:06 AM 张士军 <21620150150...@stu.xmu.edu.cn wrote: > Dear all > > I have got a crystal grown at the condition both have ion of SO4 and PO4, > and the diffraction resolution is very well, but the problem is coming: how > to tell which is which just from electron density? I think they are exactly > same. Thanks a lot !!! > > Beat Regards > > Shijun > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= ------------------------------ Date: Sat, 16 Feb 2019 16:54:37 +0000 From: "david lawson (JIC)" <david.law...@jic.ac.uk> Subject: Warning - ccp4 update 7.0.069 breaks ccp4i2 on MacBook running Mojave (v 10.14.2) Hi All, I installed the latest ccp4 update on my MacBook through the CCP4i2 update manager. After doing so, refmac appeared to be broken. I tried to restart the I2 GUI but it refused to even after a reboot. Eventually I got running again by uninstalling this update through the CCP4i update manager (i.e. the old GUI). After cloning my failed refmac job in CCP4i2, it ran without a hitch. Dave ------------------------------- Dr. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Fax: +44-(0)1603-450018 Email: david.law...@jic.ac.uk<mailto:david.law...@jic.ac.uk> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= ------------------------------ Date: Sat, 16 Feb 2019 12:49:45 -0500 From: Patrick Loll <pjl...@gmail.com> Subject: Fwd: [ccp4bb] SO4 or PO4 S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44. This is a small difference between two weak signals—unlikely to give a clear result. If you could get to the sulfur & phosphorus edges, then you could (in principle) answer this, but that’s a very hard experiment to accomplish. > Begin forwarded message: > > From: jlliu20022002 liu <jlliu20022...@gmail.com> > Subject: Re: [ccp4bb] SO4 or PO4 > Date: February 16, 2019 at 11:14:07 AM EST > To: CCP4BB@JISCMAIL.AC.UK > Reply-To: jlliu20022002 liu <jlliu20022...@gmail.com> > > How about collect data at sulfur peak. You might see anomalous peak for sulfur. > > Jinyu > > On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn <mailto:21620150150...@stu.xmu.edu.cn>> wrote: > Dear all > > I have got a crystal grown at the condition both have ion of SO4 and PO4, and the diffraction resolution is very well, but the problem is coming: how to tell which is which just from electron density? I think they are exactly same. Thanks a lot !!! > > Beat Regards > > Shijun > > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e=> > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e=> --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pjl...@gmail.com pj...@drexel.edu ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= ------------------------------ Date: Sat, 16 Feb 2019 18:55:49 +0100 From: mesters <mest...@biochem.uni-luebeck.de> Subject: Re: SO4 or PO4 Anomalous is the way to go but it helps to think about the final concentrations used..... With 50 mM PO4 (buffer) and 2 M SO4 (ammonium sulfate) most "bindin sites in quesiton" will be occupied by SO4... My 2 cents Jeroen > On Sat, Feb 16, 2019 at 4:07 AM 张士军 <21620150150...@stu.xmu.edu.cn > <mailto:21620150150...@stu.xmu.edu.cn>> wrote: > > Dear all > > I have got a crystal grown at the condition both have ion of SO4 > and PO4, and the diffraction resolution is very well, but the > problem is coming: how to tell which is which just from electron > density? I think they are exactly same. Thanks a lot !!! > > Beat Regards > > Shijun > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_webadmin-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIFaQ&c=dzukdOe-KyRBOwGgecHzPA&r=eBJx8Uo9bg3PQBubUBW3Kw&m=vntIq-VOGiJScJsr8YIvIVIhi0Nmc7GUyAXqHLSaN-c&s=ejMStPEZnfYcDDle21cSh6EgTA4aWAivYE1Cw397rxY&e= > -- *Dr.math. et dis. nat.Jeroen R. 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