[ccp4bb] Problem with getting Rfree and Rf down

[Sam Arnosti]

Hi every one

I have some crystals in the space group P3121. I collect 180 frames of data.

My crystals do not diffract better than at most 2.0 angstrom, but the Rf barely 
goes below 23%,

and Rfree also remains somewhere between 28-33%. I have tried to refine my data 
as much as I can.

I do not know whether the problem is because of the bad diffraction or 
collecting extra frames.

The structure factors are also high but they get better as the crystals 
diffract better.

Thanks

Sam

[ccp4bb] How to tell Refmac it is a fixed double bond?

[Sam Arnosti]

Hi every one

I have made a Cif file for the restraints of my ligand with Jligand, which is 
attached to my protein via a lysine-aldehyde Schiff base formation.
The problem is that whenever I run the refmac with the Cif file with torsions 
and link description, it changes the distance of the Lysine and the Carbon of 
my ligand.

The density is there, but it does not recognize it as a C=N bond and puts them 
up to 2 angstrom away from each other. 
I do not know, if I should change the link description to make the Refmac 
regonize the double bond or what else I can do.

This is the description of link in my Cif file:

_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 LYS-MER  1 NZ 2 C18   double  1.2600.020

I appriciate your help beforehand.

Regards

Sam

[ccp4bb] Crystalization in low PH

[Sam Arnosti]

Hi everyone

I have a protein that is extraordinarily stable at PH=3.0 or even 2.0.

I want to crystallize it in the  low PH and compare the differences between the 
crystals in regular PH and low PH.

I was wondering how people set up the boxes in low PH, as usual buffers are 
mostly less acidic.

Regards

Sam

[ccp4bb] Ligand Protein Connection

[Sam Arnosti]

Hi every one

I have a problem with docking my ligand into the electron density map and make 
the connections ( bonds ) with the protein.

It is a Lysine residue that makes a Schiff Base with a long chain aldehyde.

I do not know how to make the bonds and control the torsion angles of the 
ligand.

I am using the CCP4 and Coot program for refining.

Thanks

Sam