[ccp4bb] how to refine RNA with two phosphate at 5' by phenix
hi all, I have one structure contains dsRNA with two phosphate group at 5'.. I named the first residue GDP and got a cif file by running phenix.elbow. Then I refine my structure by running phenix.refine my.pdb my.cif. But the fist and the second residue do not link with each other, that is no bond between O3* of the fist residue and P of the second residue. Please give me some idea. Thanks
[ccp4bb] molecular replacement in phaser
Hi all, I got one data about 3.0 A, belong to C2 space group. There are two protein molecules and one 18-nt dsRNA per ASU. The structure of last 100aa (C-terminal) has been reported, and 400 aa at N-terminalhe has homology structure with sequence identiy 30%. I try to solve it by MR with phaser. I did rotation and tranlation with 18-nt ideal dsRNA first, then search with C-terminal model. I got about 20 sol after seaching dsRNA with TFZ 8-10.0. I use all of them to serch the first c-terminal, and second C-terminal. Ding this process, LLG keep on increasing, and TFZ is higher than 10. But all have serious clash. It looks like all the sol are wrong. Please give me a hand.
[ccp4bb] reifine metal with phenix
Hi all, The resolution of my structure is 3.1A. There are three Mg binds in this structure. I try to refine it with phenix. There are cleare extrea density before I add Mg atoms. But when I put Mg in the central of density with good coordination and try to refine it by phenix, those Mg move away.Does phenix need addiational paramters file to refine Mg and keedp it 2.1A 2.1A from it coordinated atom? Thanks. Lisa
[ccp4bb] Rwork and Rfree in Sfcheck
Hello all, I have a complex structure with resolution 2.7A The total molecular weight is 80KD, and about 10% is disordered. I refined this structure to R and Rfree 25.5% and 29.7% with CNS. I also tried refmac5, but the R and Rfree have no difference with CNS. I use sfcheck of ccp4 to check this structure. But sfcheck give the R-factor for all relections 29%. and Rfree 33%. Why sfcheck and CNS give different R and Rfree? Which R and Rfree is true? Best Lisa
