Hello Marco, I also feel that it might be due to the wrong space group because all the homologous models and alphafold model did not improve the R values. Make sure that you turn on “All possible in same pointgroup” when you run Phenix.Phaser-MR. I work with P212121 crystals a lot. Sometimes, if the diffraction quality was not good, the data will be indexed as P222, or P21212 etc, and sometimes even C2221. Try all possible in same pointgroup and see what happens. Good luck!
Zhen From: CCP4 bulletin board <[email protected]> on behalf of Marco Bravo <[email protected]> Date: Monday, February 19, 2024 at 20:17 To: [email protected] <[email protected]> Subject: [EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement [You don't often get email from [email protected]. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hello Todd, I get the best solution for p22121 space group after MR with an LLG score of 640 from phaser. and the Rfree is .4748. However after MR refinement does not lower the Rfree and it appears to make the Rfree worse. The XDS software indicates that my best solution is P21 21 2. Often Phaser MR places the solution in P 21 21 2. The helicase is a superfamily 2 helicase and is only monomeric. Its a 543aa long protein with a MW of 62Kda. It should have two RecA like domains at the core but the protein I have crystallized has a previously uncharacterized n-terminal domain responsible for tight single stranded DNA binding. I have tried different space groups manually but that resulted in clashing. I will be frank I do need to work on my crystallography background as crystal lattices, space group, and self-rotaion functions are limited. Thank you so far for your help , I will try further trimming down my search model into separate domain and trying that in the meantime. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Czg2234%40CUMC.COLUMBIA.EDU%7C09755ea7318947460db808dc31b1a714%7Cb0002a9b0017404d97dc3d3bab09be81%7C0%7C0%7C638439886434663013%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=ZVA0GLUUac8WEJ%2BNxxEiGXi2Hr%2BLUin0BFJMV6NZf0M%3D&reserved=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> This message was issued to members of https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Czg2234%40CUMC.COLUMBIA.EDU%7C09755ea7318947460db808dc31b1a714%7Cb0002a9b0017404d97dc3d3bab09be81%7C0%7C0%7C638439886434672204%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=z5rdxsCT8Q8NiimqSez9YQWpoWmUsUz9O4AiHA2J3LU%3D&reserved=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Czg2234%40CUMC.COLUMBIA.EDU%7C09755ea7318947460db808dc31b1a714%7Cb0002a9b0017404d97dc3d3bab09be81%7C0%7C0%7C638439886434677430%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=%2BXFoaNL%2BYpbuKhfo%2BoZLCMubQIt3VPoaFkccmn7WaEs%3D&reserved=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Czg2234%40CUMC.COLUMBIA.EDU%7C09755ea7318947460db808dc31b1a714%7Cb0002a9b0017404d97dc3d3bab09be81%7C0%7C0%7C638439886434682125%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=j38pLTgMKki%2BhJET%2BFNf%2F4kOYq%2F6UP1QQW5gQYkaGvg%3D&reserved=0<https://www.jiscmail.ac.uk/policyandsecurity/> ######################################################################## 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/
