Re: [ccp4bb] why I can't reproduce R based on the same program?

Hi Hailiang, I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if I try a REFMAC refinement based on the pdb file and reflection data, the initial R factor given by REFMAC should be it. The pdb file provides residual B factors with TLS

Re: [ccp4bb] why I can't reproduce R based on the same program?

Thanks for all the advices. The REFMAC PDB didn't provide ksol and bsol in the author's refinement, otherwise I would fix them in my refinement. Best Regards, Hailiang Hi Hailiang, I want to reproduce the R factor provided by PDB file. The structure was refined by REFMAC, and so I think if

[ccp4bb] Fab purification and crystallization

Again you should read the spectacular paper by Obmolova and co. where they solved the structures of three Fab-antigen complexes using MMS microseeding (seeding into random screens), starting with one hit containing clusters of needles - which could not themselves be optimized The paper is

[ccp4bb] How do I set up a Refmac5 dictionary to constrain octahedrally coordinated Ca++

Dear all, How do I set up a Refmac dictionary to constrain octahedrally coordinated Ca++? Refmac5 seems to detect the potential bond between the Ca++ and the ligands: INFO: link is found (not be used) dist= 2.229 ideal_dist= 2.320 ch:AA res: 263 GLU at:O .-ch:Ag

Re: [ccp4bb] How do I set up a Refmac5 dictionary to constrain octahedrally coordinated Ca++

Pietro, You will need to set "Make links between: All others if...residues are close only" in the Refmac GUI and write out a .cif file for the Ca-ligand distance restraints. See this link:

Re: [ccp4bb] How do I set up a Refmac5 dictionary to constrain octahedrally coordinated Ca++

Hi Pietro, There are monomer library entries for Ca in various states of coordination by water, entries, OC1, OC2,OC3 etc but unfortunately these are incomplete (no distances or angles with sd's), at least in our CCP4 installation. The entry for octahedral MG-O6, file MO6, is complete

Re: [ccp4bb] Fab purification and crystallization

Thanks everyone, I have really a lot to do now. Jurgen, yes I do separate the complex over size-exclusion column before setting trays. Patrick, Thanks for the wonderful reference. Sivaram, Thank you.It was really nice of you to send the link of your thesis.It is a wonderful gesture and I

Re: [ccp4bb] Fab purification and crystallization

Hi Ivan, Did you try using a buffer other than phosphate? Also maybe a different pH can help keeping the IgG in solution. Although papain prefers pH 6-7, it is a fairly robust enzyme and will cleave with 20% efficiency in the range of pH4-9 (Hoover S Kokes E ,1946,