Re: [ccp4bb] crystallization optimization

Actually, you should try /increasing/ the protein concentration - a lot. But be prepared to drop the precipitant concentration to almost nothing (1 or 2% isn't "low"). To understand why, look at the phase diagram and what we assume about vapour diffusion. (Which I'm assuming is what you're

Re: [ccp4bb] crystallization optimization

Dear Patrick, You may reduce the protein concentation, as well. Another option could be the *streak seeding* by exploiting the drop of your initial condition. Good luck, V.T. On Mon, Jul 10, 2017 at 7:17 PM, Patrick Shaw Stewart wrote: > > Microseed them into two or

Re: [ccp4bb] Problem with a cell content

Absolutely agree Eleanor On 11 July 2017 at 22:06, Keller, Jacob wrote: > Still seems to me that the resolution could and should be pushed a little > further at least—CC1/2 is still high, completeness is good, I/sigma also is > good. Why not extend a little further,

Re: [ccp4bb] Problem with a cell content

Still seems to me that the resolution could and should be pushed a little further at least—CC1/2 is still high, completeness is good, I/sigma also is good. Why not extend a little further, say to where one of these values gets too low? Might improve the maps a bit. JPK From: CCP4 bulletin

Re: [ccp4bb] Problem with a cell content

That makes sense then - you have solved it am sure. Eleanor On 11 July 2017 at 20:36, Koromyslova, Anna < a.koromysl...@dkfz-heidelberg.de> wrote: > Sorry for the confusion, NCS was found only in a dataset where the cell > dimensions were twice bigger regardless of the sp, and with a dimer as a

Re: [ccp4bb] Problem with a cell content

Sorry for the confusion, NCS was found only in a dataset where the cell dimensions were twice bigger regardless of the sp, and with a dimer as a solution. The solvent content was the same. Peak Distance Vector 73.3% 143.8Å: FRAC +0.000 +0.000 -0.500 (ORTH -0.00.0 -143.8). There was

Re: [ccp4bb] Granada Crystallization Boxes?

Triana is no longer making or selling them On Tue, Jul 11, 2017 at 1:39 PM, Diana Tomchick < diana.tomch...@utsouthwestern.edu> wrote: > You can continue to buy new ones from Tirana Science & Technology, which > is a Spanish company. > > http://www.trianatech.com/index.php?option=com_content; >

Re: [ccp4bb] Granada Crystallization Boxes?

Sorry, that’s Triana Science & Technology (darn automatic spell-check!). Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX

Re: [ccp4bb] Granada Crystallization Boxes?

You can continue to buy new ones from Tirana Science & Technology, which is a Spanish company. http://www.trianatech.com/index.php?option=com_content=article=65=88=en Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry

Re: [ccp4bb] Problem with a cell content

So SG could be P31 2 2 What is the height of NCS vector v origin? Eleanor Look at hklview to see hk i sections. Obviously all l = odd will be weak. On 11 July 2017 at 19:12, Koromyslova, Anna < a.koromysl...@dkfz-heidelberg.de> wrote: > Dear Eleanor, > > > > NCS translation vector = 0 0

Re: [ccp4bb] Problem with a cell content

Dear Eleanor, NCS translation vector = 0 0 -0.5 in the final sp P6222, and in P622 or C121. All had the same solution. The protein tends to form a homodimer and if I use P1 space group molecular replacement can find several dimers, there is no translational ncs found during MR, but still

[ccp4bb] Granada Crystallization Boxes?

I have recently found out that these are no longer being manufactured or sold commercially. But, as fortune has it, we have just been funded to fly some large quartz capillaries crystallization experimente up to the International Space Station for neutron crystallography. Our experimental design

Re: [ccp4bb] Problem with a cell content

Anna, Eleanor is raising very important question: if you have NCS then there should be another similar entity in the asu. Have you detected off origin peak while using your final P6222 or lower sg? From: Koromyslova, Anna [mailto:a.koromysl...@dkfz-heidelberg.de] Sent: Tuesday, July 11, 2017

Re: [ccp4bb] Problem with a cell content

Dear Vaheh and Phil, Sorry, I was a bit misleading – antibody fragment I used is a nanobody (VHH, 15kDa). I was worried about the cell content because when I started the pdb deposition, there was a warning that solvent content is expected to be below 80%, so I thought maybe I missed a correct

Re: [ccp4bb] Problem with a cell content

This is very strange . If you have a large non- crystallographic translation vector you would expect either to have two molecules in the asymmetric unit or your one molecule must have two very similar domains? What is the n-c translation vector? Could you have assigned too high symmetry ? SG

Re: [ccp4bb] Problem with a cell content

Похоже, что вы уже решили структуру. Почему вас беспокоит плотность ваших кристаллов? Кристаллы бывают разные. First of all Fab by itself is already almost 50 kDa, so complex with antigen should be more than 50 kDa. Because you already solved the structure calculate the molecular mass based on

Re: [ccp4bb] Problem with a cell content

Hello Anna You've already found the correct number of molecules in the asymmetric unit. 21% Rwork is a quite respectable value for a structure at this resolution, and while 80% solvent is a relatively rare occurrence it's not unprecedented (a couple of years back I did one at 3.0Å with 75%

[ccp4bb] Problem with a cell content

Dear CCP4 members, I am working on a structure of a protein in complex with an antibody fragment (approx. 50kDa together). Molecular replacement with closely related proteins always comes up with one complex in the asymmetric unit, although MW of protein to which Matthews applies is 125kDa and

[ccp4bb] AW: [ccp4bb] Inquiry - active and non-active state in alternatives

dear petr, several phytochrome structures seem to represent mixed-state crystals. best, jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Petr Kolenko Gesendet: Dienstag, 11. Juli 2017 16:00 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb]

[ccp4bb] Inquiry - active and non-active state in alternatives

Dear colleagues, We are working on a paper, where we want to discuss our crystal structure. We have determined structure of non-active state first (much easier). Than we tried to convert the protein into active state by soaking (direct crystallization not possible). We have observed more

[ccp4bb] Postdoctoral position in cryo-EM, Harvard Medical School

Dear all, The Brown lab at Harvard Medical School has an opening for a postdoctoral scientist. The lab uses the latest developments in cryo-EM to understand biological processes at the molecular level (e.g. Nature 524, 493–496 and Science 346, 718–722). The project will involve investigating

Re: [ccp4bb] SHELXE: peptide occupancy refined to negative value

Dear Andreas, did you try the option '-t' to make SHELXE try harder, or other building related options (take a look at the SHELX web page for talks and presentations). Can you make use of the phases without model building? (sfall) Since you seem to get a PDB-file, could you use the

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello again, Back in 2001 people still remembered the difference between Rsym and Rmerge. 16 years later people seem to have forgotten. I will try to dig even more ancient references… Archaeology is the name of the game. http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html Cheers, Fred.

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello Frederic. Interesting. Have you got some reference on this to share? James  Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email:

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello, I think this needs a little bit of crystarchaeology. Rmerge and Rsym used to be different. This was at a time when data sets were typically collected from several crystals. Pre-cryo cooling, with data recorded on photographic film (Arndt-Wonacott cameras). Rmerge = agreement R-factor