Re: [ccp4bb] how to reduce protein solubility

Hi Francesca, It may be worth trying D2O (rather than H2O) in the final protein buffer. It sometimes causes problems in NMR experiments. One of my colleagues had success with this approach. Crystal screening will need to be done under oil (micro batch) to stop losing D2O by vapor diffusion.

Re: [ccp4bb] P3212--1's in Space Group Names?

the same as the 1 in P1 ;-) seriously, if you look at space group names: 143 P3 144 P31 145 P32 149 P312 151 P3112 153 P3212 150 P321 152 P3121 154 P3221 the 1s in 149 to 154 are necessary to differentiate them all. On 18 Feb 2015, at 04:51, Keller, Jacob wrote: Dear

[ccp4bb] how to reduce protein solubility

Hi Francesca, since your protein is expressed in eucarytic cells, glycosylation might be an issue. Glycosylation usually enhances the solubility and can influence the crystallisation negativly because of high flexibility. There are commercially available deglycosylation kits. You can try

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Re: [ccp4bb] P3212--1's in Space Group Names?

At the risk of muddying the waters further, the difference between 312 and 321 is that the 2-fold normal to the 3-fold is along the diagonal of the ab face in 312, while it is along the a (or b, by equivalence) in 321. The 1 is definitely no place holder. It has a very significant meaning. The

Re: [ccp4bb] P3212--1's in Space Group Names?

...The 1 is definitely no place holder. It has a very significant meaning. Not sure why place holders are inimical to significance. I think you are saying that the 1 tells you there is no rotation here, like the 0 in the number 201 tells you there are no tens in that number. I call that a place

Re: [ccp4bb] Poor experimental phases for a largish structure...

Dear William, In a similar circumstance, we cut out the density from one crystal, and used that to solve the structures of non-isomorphous crystals by molecular replacement. At this point, we had an envelope (needed to cut out the density), initial maps, and operators to place one copy of the

Re: [ccp4bb] P3212--1's in Space Group Names?

Laurent Maveyraud laurent.maveyr...@ipbs.fr writes: this is explained in details in table 2.2.4.1 of vol A of International Tables of Crystallography (p 18 in my edition). For trigonal/hexagonal, the primary direction is along c, along the 3-fold (6-fold axis). It's the same in tetragonal

Re: [ccp4bb] Odd diffraction

Dear Fang Lu, These spots are from a small molecule crystal. There is one very short axial length (large distance between reciprocal lattice rows) and one quite long axis (the spots are close together in the straight reciprocal lattice row near the bottom of your diffraction pattern) You can

Re: [ccp4bb] P3212--1's in Space Group Names?

Well let me further muddy the waters by insisting that the 1 IS DEFINITELY a place-holder, telling you that there is no rotation (greater than 1-fold) along the a or b axes, and that the 2 therefore refers to 2-fold rotation along the next axis, the ab diagonal (no the -a,b diagonal which is

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Re: [ccp4bb] Odd diffraction

The spots at the very edge is around 2.5A. 2015-02-18 12:15 GMT+00:00 Fang Lu fangluwork...@gmail.com: Hi all, I got this odd diffraction. Not sure what it is, detergent or protein? Any ideas? The crystallisation condition is 2.4M Sodium Malonate. GF buffer contains HEGA-10,Tris,

Re: [ccp4bb] P3212--1's in Space Group Names?

Dear Dear Crystallographers, Thanks very much to all who replied on and off the list—I feel I have to express my continuous admiration and gratitude to the folks who respond to these questions. I am not sure where there is a listserve like CCP4BB! Anyway, in the current issue I have gotten to

Re: [ccp4bb] P3212--1's in Space Group Names?

Hmm, placeholder for me does not seem to emphasize enough the role that this number plays in the space group names. My understanding (but I fail to remember where I read this ...) is that the first number is the order of the rotation (i.e. 6,4,3,2 or 1) of the unique unit cell axis (often the

[ccp4bb] Odd diffraction

Hi all, I got this odd diffraction. Not sure what it is, detergent or protein? Any ideas? The crystallisation condition is 2.4M Sodium Malonate. GF buffer contains HEGA-10,Tris, KAcetate, MgAcetate, EDTA and DTT. Protein size is around 100kDa. Thank you for your time. Fang [image: 内嵌图片 1]

Re: [ccp4bb] P3212--1's in Space Group Names?

Yes, the 1 in these space group names is the same as the 1 in P1. 1 is the identity symmetry operator. For a trigonal space group (and hexagonal) the symmetry operators are given in an axis order of (z) (a,b) and (i) where i is defined by the ab vector (the ab diagonal) So, for example in

Re: [ccp4bb] P3212--1's in Space Group Names?

Hi, this is explained in details in table 2.2.4.1 of vol A of International Tables of Crystallography (p 18 in my edition). For trigonal/hexagonal, the primary direction is along c, along the 3-fold (6-fold axis). It's the same in tetragonal (obviously for the 4-fold axis !).. The

Re: [ccp4bb] P3212--1's in Space Group Names?

Well, I meant no harm to the poor 1 by calling it a placeholder, but that in the case of P3212, the 1 is simply to tell you that there is no rotation about the second axis but is instead about the third. Saying okay, nothing here amounts to being a place-holder to avoid ambiguity in assigning

[ccp4bb] The discrepancy for determination of Ramachandran outliers by Coot and MolProbity

Dear All, It often finds for the Ramachandran favored determined by Coot, MolProbity regards as Ramachandran outliers. There are earlier posts regards Coot and MolProbity has different database for the determination of the Ramachandran plots. Then will you please let me know the correct way to

Re: [ccp4bb] Poor experimental phases for a largish structure...

Hi, If your Hg dataset is not isomorphous with the SeMet you can cut out some density and use cross-crystal averaging (molecular replacement using electron density) to transfer the Hg phases to the Se dataset. You can then try using an anomalous difference fourier map to find more or weaker