Various (all depressing) possibilities.. You don’t say what the sequence ID to the models us
Your protein is flexible with poor fit to the available models. How well do those overlap? The bioinformatics tools in i2 give you pictures showing this. Look at them and see if there are sensible places to divide models up for the search. You have crystallised the wrong protein - not common but it does happen.. I use cco4i2 fir most things and there is a MR option there to use SINBAD . That checks against the pdb whether there is a deposited structure that has a) your point group and cell, then whether that model fits your data. Next go back to the data processing. The ccp4i2 report needs to be read carefully. Is the data poor? Inspect the graphs and warning messages.. What is the Rmerge? Are there bad batches? There is a graph showing the variation against batch.. if there are wild variations you may need to exclude some batches.. It will suggest there might be twinning , look st the Wilson plot graphs . Is there non- crystallographic translation? ( not harmful but if the translation is (x,y,z=1/2) say then the space group selection is problematic - the fact that all l=2n+1 ( used to suggest the soacegroup is P2i2i21) might be caused by that translation.. Then how many copies of your protein can fit into the crystal lattice? There is a task - “import sequence “ then another “define AU contents”. You input sequence and experimental diffraction data and it tells you if one or two or many molecules can fit. That is only a guesstimate but if the cell can hold many copies the MR search will be more challenging. If there could be several copies a self rotation function ( in ccp4i2 part of the data processing folder) might tell you there is a dimer ? Trimer? Etc .. but you say you expect a monomer.. The good news is that you have a solution with r factors below 0.5. Have you tried rebuilding from that starting point? In some cases Buccaneer/ modelcraft can take that model, discard the worst defined bits and rebuild the model. Not terribly likely to succeed with 2.8A data and a poor MR solution but worth a try.. On Tue, 20 Feb 2024 at 01:30, Gong, Zhen <zg2...@cumc.columbia.edu> wrote: > 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 <CCP4BB@JISCMAIL.AC.UK> on behalf of Marco > Bravo <mbrav...@ucr.edu> > *Date: *Monday, February 19, 2024 at 20:17 > *To: *CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject: *[EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement > > [You don't often get email from mbrav...@ucr.edu. 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 > ######################################################################## 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/
