Hello Arpita, If you look up the f" values of various elements ( http://www.bmsc.washington.edu/ ) you will see that there are elements which will give you more or less signal at your wavelength of 1.5412 eV. For example, phosphate can be seen to have an f" value of about 0.43 e at that wavelength/ energy. As a counter example, Na only has ~0.1 e at that energy. Assuming you have reasonable completeness and multiplicity in your data, you should be able to see that kind of difference (if it is there). Best regards, tom ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Arpita Goswami <bt.arp...@gmail.com> Sent: Wednesday, December 20, 2023 3:53 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Query on density fitting to phosphate
You don't often get email from bt.arp...@gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi, Thank you all for the replies. As suggested, this is the residual positive difference density after putting water and refinement in coot-refmac: https://i.postimg.cc/DfbrbDZm/Screenshot-from-2023-12-19-16-39-38.png Does this look like any of the three phosphate ions? Two sides are similar, while one side is a little longer than others. H2PO4- has single negative charged Oxygen. The alternate conformation of the said arginine may not be possible as it is situated quite far from aspartate. As suggested both H2PO4- and HPO42- should dissociate to phosphate ions. Is it possible some H2PO4- will remain undissociated at pH 6.2 at low temperature like 4 degree centigrade (crystallization condition)? The pKa of H2PO4- dissociation is 7.2. Thank you for the suggestion of an anomalous map. We used 1.5412 A wavelength for data collection. So for an anomalous map for Phosphorus we do not have the data for now. I tried sodium and potassium ions. Sodium gives residual positive difference density as seen in water, for potassium also likewise. Also presence of lysine at close distance is not helpful for them. Waiting eagerly for your reply. -- Thank you. Best Regards, Arpita On Mon, Dec 18, 2023 at 7:01 AM Joel Tyndall <joel.tynd...@otago.ac.nz<mailto:joel.tynd...@otago.ac.nz>> wrote: Have you tried sodium? From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Arpita Goswami Sent: Sunday, December 17, 2023 11:47 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Query on density fitting to phosphate Dear All, Hope you all are doing well. The density in the image (in link below) is fitted with PO4 ion, although the crystallization condition has both mono and dihydrogen phosphate which is not fitting without hydrogen. But the resolution is 2.5 A, so hydrogen may not be put in, or is there any way to do so? Otherwise placing water is the final option. https://i.postimg.cc/4N7q2K0p/Screenshot-from-2023-12-17-16-07-07.png Also the density is quite close to Aspartate, so PO4 may not be right. Can it be dihydrogen phosphate as two positively charged residues (Specially the lysine) are also nearby to neutralize positive charge? Other ions in the crystallization condition are Cl-, K+ and Na+. These are not put as both aspartate and lysine are at comparable distances from the density. The pH is 6.2 in which dihydrogen phosphate is reported to interact with aspartate (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5855859/). Waiting eagerly for your reply. -- Thanks and Merry Christmas in advance. Best Regards, Arpita ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
