[ccp4bb] Alignment of Electron Density Map for structures that have different space groups

2009-09-06 Thread Milya Davlieva
Dear all, I need to make a figure which needs to consist of 2 aligned pdb files and their electron density maps for the structures of two mutants (with different space groups). I'm able to do this when there are two structures that have the same space group. Could, you, please, help me to

Re: [ccp4bb] Adding a transmembrane segment

2009-09-06 Thread Artem Evdokimov
Hi, Could you clarify your request a bit? Generally speaking if you allow the ectodomain to have a membrane anchoring segment it will 'compromise' solubility since the resulting protein most likely requires special treatment (detergents) in order to be soluble. There's also the matter of the se

Re: [ccp4bb] Adding a transmembrane segment

2009-09-06 Thread Pascal Egea
Hi,if you add the TM segment, I would expect that the protein will then get targeted to the membrane and hopefully inserted correctly. My guess is that you will have to treat your protein as a membrane protein or a membrane-anchored protein...which means prepare a membrane fraction, use detergent a

Re: [ccp4bb] Devices Suitable to Concentrate Protein Solutions in Liter Scale

2009-09-06 Thread Pius Padayatti
may be diafiltration devices might work for you. the membranes are kind of expensive but we had used this effectively to reduce the volume of cell culture media where we had secreted proteins in large volumes of culture media. here is a link http://www.spectrapor.com/lit/hfdial.pdf padayatti On

Re: [ccp4bb] Devices Suitable to Concentrate Protein Solutions in Liter Scale

2009-09-06 Thread Pius Padayatti
may be diafiltration devices might work for you. the membranes are kind of expensive but we had used this effectively to reduce the volume of cell culture media where we had secreted proteins in large volumes of culture media. here is a link http://www.spectrapor.com/lit/hfdial.pdf padayatti On

Re: [ccp4bb] Devices Suitable to Concentrate Protein Solutions in Liter Scale

2009-09-06 Thread Wu, Zhongren
If you want to just reduce the volume/concentrate proteins, you can use Millipore's Stirred cell (high-output stirred cell, 2,000 ml capacity). Zhongren Wu From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Xuan Yang Sent: Thursday,

[ccp4bb] Adding a transmembrane segment

2009-09-06 Thread aka akaka
Dear All I am working with a viral protein that contains an ectodomain, a TM segment and a cytoplasmic region. I was wondering if there is a general strategy that allows the addition of the transmembrane segment to the ectodomain without compromising solubility and secretion. Thanks Dr. R. D

Re: [ccp4bb] How to get rid of the skin in the screening drop

2009-09-06 Thread Shu XU
Lower the concentration did help a little bit. I didn't the 6 mg/ml setups, but still got some skins. You are right the skins are more likely to find in the condition of PEGs...but also find in other conditions. Lower the conc. of PEGs is a good advice, and I'll try it. Thanks. Shu On Sun, Sep 6,

Re: [ccp4bb] How to get rid of the skin in the screening drop

2009-09-06 Thread Jeremiah Farelli
This happened to me previously, and the only thing that worked for me was to lower the protein concentration. I was setting my protein up at 10 mg/mL, only to find skins on nearly all the drops. I would damage the crystals trying to get them out of the drops... I lowered my protein concentration

[ccp4bb] stabilizing solution

2009-09-06 Thread james09 pruza
Dear CCP4bbers, Please comment on the stabilizing solution for seed stocks. If the crystal is in 30% MPD and coming after 2-3 days, what should be the stabilizing solution for seeding. Thanks. James