Re: [ccp4bb] An unknown but strong positive electron density in my crystal

Hi everyone, Thank you for your replies. I have uploaded the figures to a website. The link is here: yueliblog.webador.co.uk Best wishes, Yue To unsubscribe from the CCP4BB list, click the following link: https://www.j

[ccp4bb] high TFZ score but 50% of Rfree

Dear all, I have several datasets (one best resolution reaching 2.2A), giving C2 space group, two molecules in an asymmetry unit (65.1% of solvent content).  When running MR using a template (<20% sequence identify to the target molecule), I got a solution with high TFZ (23.7) and LLG (842). How

[ccp4bb] precipitation of deglycosylated protein

Hi everyone, Recently, I obtained a soluble glyco-protein. Unfortunately, after I added PNGase or Endo Hf to remove the glycans, the deglycosylated protein is precipitated. Is there any method to avoid this kind of precipitation? Thanks, Simon  

[ccp4bb] pointless and HKL2000

Hi everyone, I would like to us pointless in CCP4 to check the laue group of a crystal. Since pointless needs unmerged data, my question is how to generate the unmerged data for pointless from HKL2000 ? Thanks, Simon

[ccp4bb] low B factor for water

Hi all, When I refined one of my structures in refmac and cns, I found some water molecules having low B factor (i.e < 10). Should I omit these water molecules from the structure ? The overall B factor is 35.3 Thanks Simon

[ccp4bb] insoluble ligand

Hi all, I have one ligand which is insoluble in water, and I would like to co-crystallize it with my protein. Is there any other method except for dissolving it in DMSO ? Thanks Simon

[ccp4bb] skin on a drop

Hi All, As we know, there is a skin on a crystallization drop, especially when the drop contains PEG. Does anyone know what the skin is, a degraded protein ? How to prevent it ? Thanks Simon

[ccp4bb] removal of sulfate ion from the active site

Hi all, I have crystals of the apo enzyme growing from 1.7M ammonium sulfate condition. After soaking with 10mM ligand (substrate analog) which has a phosphate group, the ligand did not enter the active site of the enzyme because of the competition of sulfate ion and phosphate group. So I am wond

[ccp4bb] degassed commercial screen kits

Hi All, I am working on an Fe-S cluster protein. Generally, I do the initial screen using the commercial kits, like Hampton screen kits, etc.. Do you have any experience in degassing these commercial kits before setting up the trays ? How to deal with the solutions in the kit which contain orgainc