Hi Anirban, Never thought someone will ask for image of 'ugly' crystals, but fortunately I have found some saved pictures which is more than 8 years old!
I think I have a perfect example. The pictures can be found in the folder by following the link: https://drive.google.com/drive/folders/0B1M5Wq4437-CN0pLWXdOUG44MlE?usp=sharing These ugly crystals diffracted to 1.95 Å as opposed to some nice looking crystals (grown in different condition) that diffracted to quite lower resolution. The structure from these crystals have PDB ID is 2XQ0 ( https://www.rcsb.org/structure/2XQ0). The structure is described in JMB journal ( https://www.sciencedirect.com/science/article/pii/S0022283610012969?via%3Dihub ). Best wishes, Mahmudul Lund Sweden On Fri, Jun 29, 2018 at 8:57 AM Janet Newman <janet.new...@csiro.au> wrote: > Hi Anirban, > > Single easy example to find (see attached images) - gorgeous crystals - > sub 3A (grown in sodium malonate) > Lozenge crystals - better than 2A (grown in ammonium sulfate) > > (Barbiturase protein ) > > Cheers, Janet > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Debanu Das > Sent: Friday, 29 June 2018 4:36 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Please share your experience about "ugly" crystals > showing good diffraction > > Hi Anirban, > > At JCSG, we subjected ~180,000 crystals from ~3500 unique/novel > proteins/complexes to X-ray diffraction screening, resulting in >1500 > novel structures in the PDB at an average resolution ~2.0A. In theory, > if we had the bandwidth now to sort through all that data to pull out > images of the mounted crystals and their diffraction quality, we could > probably get some good analysis done on this. > > However, as an alternative, I can certainly provide some examples that > we have dealt with recently that I hope will add substance to the > anecdotes to motivate your trainees! > > a) For one protein, our first crystals were oval shaped, without sharp > geometry/edges, much like a pebble. We got a high quality 1.9A > structure out of it. Subsequent optimization led to much nicer looking > crystals with nice shapes and we collected ~50 data sets from them all > resulting in ~2A structures so not much improved compared to the > initial visually poorer crystals. > > b) For another protein, crystals grow nicely but some of the crystals > remain suspended in solution whereas other settle to the bottom and > stick. For the ones which stick, some can be dislodged by gentle > prodding with a nylon loop while harvesting and they result in (along > with the ones that are not stuck) in ~1.8-2A structures. For the ones > which are stuck and cannot be gently dislodged, a nudge with a plastic > tip (out of desperation!) is sufficient to dislodge them, and they > retain their nice visual appearance and shape, but have total loss in > diffraction. > > c) We see this too for crystals soaked with ligands. In some cases > after soaking the crystals appear fine but suffer in diffraction > quality, and in some cases they appear to have suffered visually but > result in usable data sets/structures. > > So at the end of the day there are crystals that appear nice but do > not diffract well and there are crystals that do not appear nice but > lead to good/usable structures. So it's all about inner beauty. Never > give up on crystals/crystal optimization without testing them by > X-rays. > > Best, > Debanu > > On Thu, Jun 28, 2018 at 5:07 PM, Anirban Banerjee <ani...@gmail.com> > wrote: > > > > Dear all, > > > > Apologies for the non-CCP4 related question. > > > > If you have concrete experience about visually unappealing, i.e. ugly > > crystals ( your own take on ugly is fine) diffracting better than > > comparably similar sized nicer looking crystals of the same protein, will > > you please share here ? Even better if that led to a published structure. > > Might you also have pictures ? > > > > We have all heard anecdotes about not using visual appearance to judge > the > > quality of crystals as far as their ability to give good diffraction > data is > > concerned but I am trying to gather some concrete pointers here to > motivate > > trainees. > > > > Thanks very much for any help. > > > > Best, > > > > Anirban > > > > P.S. I know that there is probably a lot of thought and wisdom on this > this > > specific topic but I am really looking for actual experience. > > > > ________________________________ > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
