 |
 |
Nukri poses a very good question. Fortunately for me, I think others are answering it: Daniel Bonsor has emailed me a couple of relevant references, which I reproduce here: ----------------- Acta Cryst. (2010). F66, 346-351=20 Crystallization and X-ray diffraction studies of cellobiose phosphorylase from Cellulomonas uda20 The space group was originally P21. During collection the crystal moved out of the beam (and possibly the cyrostream). Upon recentering, the space group was found to be P212121 Acta Cryst. (1998). D54, 448-450=20 Crystallization and preliminary X-ray analysis of thiaminase I from Bacillus thiaminolyticus: space group change upon freezing of crystals At room temperature the space group was P212121 but upon freezing the space group changes to P21212 ----------------- The best example of temperature-induced space group changes I know of is a table of "solid-solid phase transitions" inorganic crystals Eddie Snell put together: http://bl831.als.lbl.gov/~jamesh/pickup/Snell_SG_change_table.pdf and he just provided me with the appropriate reference for that: Tomaszewski, P.E.: Structural Phase Transitions in Crystals, I. Database, in: Phase Transitions 38(1992)3,127-221 So, since temperature-induced space group changes are so "common" in small-molecule crystals, I expect that they may be even more common for larger structures. Some of the best work I am aware of on temperature-dependent structural changes in proteins in general was done in Brian Matthews's lab: Juers & Matthews (2001) J. Mol. Biol. 311, 851-862. Juers & Matthews (2004) Q. Rev. Biophys. 37, 105-119. Although I don't think they specifically mention space group changes, it is not hard to imagine how changes in conformation like this could induce them. As one brilliant engineer put it: "The more they overwork the plumbing, the easier it is to stop up the drain". Sadly, I don't think there is a comprehensive review of phase change phenomena in protein crystals. Probably because there are few investigators who have a comprehensive collection of purified proteins, and because such "anecdotes" seldom survive to the final version of peer-reviewed papers. -James Holton MAD Scientist On 9/30/2010 7:13 AM, Sanishvili, Ruslan wrote: > Folks, > I am not questioning James - I just would like to see some papers if > there are any so I can use them as reference. > Cheers, > N. > > Ruslan Sanishvili (Nukri), Ph.D. > > GM/CA-CAT > Biosciences Division, ANL > 9700 S. Cass Ave. > Argonne, IL 60439 > > Tel: (630)252-0665 > Fax: (630)252-0667 > [log in to unmask] > > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > [log in to unmask] > Sent: Thursday, September 30, 2010 9:06 AM > To: [log in to unmask] > Subject: Re: [ccp4bb] difficult P1 crystal > > no publication springs to mind immediately (often apparently of non > scientific relevance) but I have seen it on numerous occasions so fully > support James' comment. > > All you need to do is read the IUCr tables (yes, boring, but > occaisionally useful) to see how simple it actually is. > > Liz > > ________________________________ > > From: CCP4 bulletin board on behalf of Sanishvili, Ruslan > Sent: Thu 30/09/2010 15:03 > To: [log in to unmask] > Subject: Re: [ccp4bb] difficult P1 crystal > > > > Hi James, > Can you, or anybody else, point me to a publication where "...not that > uncommon for one or more crystal symmetry operators to "collapse" upon > cryo-cooling..." > Thanks, > Nukri > > Ruslan Sanishvili (Nukri), Ph.D. > > GM/CA-CAT > Biosciences Division, ANL > 9700 S. Cass Ave. > Argonne, IL 60439 > > Tel: (630)252-0665 > Fax: (630)252-0667 > [log in to unmask] > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > James Holton > Sent: Thursday, September 30, 2010 8:43 AM > To: [log in to unmask] > Subject: Re: [ccp4bb] difficult P1 crystal > > Yes, this sort of thing happens a lot more often than one might think, > but people who have crystals with such "high-copy asymmetric units" tend > > to not solve them. Hence, they don't end up in the PDB. In cases where > > the structure is eventually solved, it is usually done by finding an > alternative crystal form. At least, that is what I usually see when > people bring these things to the beamline. Yes, the high NCS sounds > like it would be really cool, but the reality of high-copy ASUs is that > they are particularly prone to radiation damage problems. Not because > of any special chemistry, but because the big ASU means that a complete > data set from a single crystal requires collecting a lot of photons (see > > Holton& Frankel, 2010, and http://bl831.als.lbl.gov/xtalsize.html), and > > that high-copy ASUs tend to also have non-isomorphism "issues" (making > it difficult to merge data from many crystals). Yes, the NCS advantages > > "cancel" this hindrance, but only at a much later stage (after you have > found all the sites). That, and I think there is some psychological > barrier to building and refining 24 copies of the same thing! > > Why do high-copy ASUs happen? Sometimes they occur naturally, like > certain invertebrate hemocyanins where one molecule contain dozens to > hundreds of copies of a single domain. Bart Hazes can tell you all > about these! > > However, it is also not that uncommon for one or more crystal symmetry > operators to "collapse" upon cryo-cooling (or other forms of crystal > abuse). I have seen this a lot! There are many examples of > nearly-crystallographic NCS in the PDB, many of which I suspect are > cryo-cooling artifacts. Doesn't change the structure all that much, but > > should you choose to "go with it" you do have to be VERY careful with > NCS like this! It is very easy to invalidate the Rfree. An extreme > example is taking a crystal that is actually P2, but instead processing > it as P1, picking a random "free" set, and refining with a twofold NCS > operator. You will find that Rfree will drop like a rock and become > essentially equal to Rcryst. This will be the case even if the > structure you are refining is totally wrong! This is because every > "free" reflection actually has an "NCS symmetry mate" in the working > set. There are an alarming number of cases like this in the PDB, but I > will not name names here. > > What is the "result" that makes you think your crystal is not > tetragonal? > > -James Holton > MAD Scientist > > On 9/30/2010 4:54 AM, Mario Milani wrote: >> Dear all, >> i have a 30 kDa protein that crystallize so far in three different > conditions but with the same space group. It initially looks like > tetragonal (I4, a=141, b=141, c=208) and then results triclinic (P1, > a=141, b=141 c=144, alpha=119, beta=119, gamma=90), hosting about 24 > mol. in the unit cell. Other data: self rotation shows the presence of 4 > peaks with chi=180; molecular replacement shows the presence of a > pseudo-translation peak; DLS made at protein concentration close to > crystal growth conditions shows a Rh compatible with something like a > tetramer with low polydispersity (about 15%). Do you have any experience > with similar 'asymmetric' associations? Do you have any suggestions, > beside the addition of ligands to the crystal growth conditions, in > order to get a 'simpler' crystallographic assembly? I have some models > (with sequence identity less than 25%) in order to try MR but all trials > so far did not solve the structure (using balbes, molrep, phaser and > epmr). Any suggestion is welcome. >> Thank you, >> >> Mario Milani