Re: [ccp4bb] Calcium ions in enzymes

staph nuclease On 31 May 2013, at 6:25 AM, Wei Liu wrote: Dear all, As we all know, many proteins contain calcium ions. Does anyone know if there are reported cases where calcium ions play a catalytic role rather than a structural role in enzymes? Best Wei Liu

Re: [ccp4bb] Puzzling observation about size exclusion chromatography

If your protein elutes very late, that means it's binding to the column matrix (so all estimates of size go into the trash). Check to see that the ionic strength of buffer is reasonable (equivalent to, say, 150 mM NaCl). If so, then the only solution is to go to a different matrix type. Pat On

Re: [ccp4bb] off-topic: bug busting

I'm joining the pig-pile on the Emulsiflex. I like it because: a. The folks at Avestin are very helpful (they're Canadian--just naturally nice) b. It'll break yeast as well as E coli c. It seems pretty gentle to me (we pack it in ice, so there's negligible sample

Re: [ccp4bb] Determining concentration of membrane protein

No, because Bradford is based on the increase in absorbance when the dye moves from a hydrophilic environment to a hydrophobic one (like the protein interior, or like the interior of a micelle). When detergents are present in excess of their CMC, the change in absorbance from partitioning into

Re: [ccp4bb] question on charge charge interactions

Two Arg side chains stack next to each other in ferritin and in GST (see, for example, Arg-59 and its symmetry mate in 3F33). I expect there are other examples, but these two come readily to mind. Cheers, Pat On 27 Mar 2014, at 7:11 PM, Tom Peat wrote: Hello All, I am appealing to the

[ccp4bb] Fwd: [ccp4bb] : MTZ for a protein fragment and R factors, Masking and Maps

George, Remember that scattering from every point in the cell contributes to every reflection; the R-value is a global metric of agreement between the model and the data. Hence, calculating the R-value for a few selected residues is not a sensible thing to do, unless you want to ask how well

Re: [ccp4bb] How to transfer non-frozen crystals with less disturbance?

You can cut a small piece of sponge and put that into the reservoir; this prevents the reservoir buffer from splashing up into the drop. The sitting drops should be reasonably safe, but the 10 uL hanging drops are big; they'll be vulnerable to falling off if the tray is jarred. Good luck! Pat

Re: [ccp4bb] very informative - Trends in Data Fabrication

Ron makes an excellent point. Many institutions devote far more energy to limiting risk than to doing the right thing. This leads administrators to a frightening, but logical conclusion: The less science we do, the less chance of our doing something that could invite a penalty on the

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

Well, it is clear from this comment that in different fields there are different rules... . In macromolecular Xtallolgraphy, where some people deal with biologists from biomedical sciences, the impact of journals is an important aspect during evaluation and, unfortunately, pre-publication

Re: [ccp4bb] Anaerobic glovebox crystal cryo-cooling

Think about hyperquenching (a high-falluting name meaning to use a stream of gas to blow off the cold layer that accumulates above the surface of the liquid nitrogen). We just blow some nitrogen at the surface of the dewar, very low tech...but it works. Importantly, you can use a more leisurely

Re: [ccp4bb] selective protection of C-terminal carboxylate

If you express the protein as an intein fusion you can make a C-terminal thioester, which you can then modify quite specifically with various reagents . Pat On 25 May 2012, at 10:00 AM, Sebastiano Pasqualato wrote: Dear all, is anyone aware of a way to selectively protect the carboxylate at

Re: [ccp4bb] Mercury phenylglyoxal

I second the mythical conclusion. We also tried to make it and failed 10-15 yrs ago (we came up with the di-iodo compound, if I recall). Many of these organomercurials are really tough to handle; I suspect that even if we had succeeded in making the desired compound, it would have been as

Re: [ccp4bb] OFF TOPIC: recommendations for High Pressure Homogenizers

We have an Avestin C5 that's about 10 yrs old, and pretty much everything that Bert said is also true for us. The instrument works great for bacteria; it can also break yeast, but the pressures required are at the upper limit of its capabilities, so everything needs to be in tip-top condition.

Re: [ccp4bb] Convert cbf to png/tiff?

adxv reads cbf images, and can save them as postscript (actually, it's supposed to be able to save the image as tiff as well, but at least on my version of the program that feature doesn't work). Pat On 10 Jan 2013, at 3:36 PM, Frank von Delft wrote: Hello all - anybody know an easy way to

[ccp4bb] refinement hanging--what am I missing?

Hi all, Here is a problem that's been annoying me, and demanding levels of thought all out of proportion with the importance of the project: I have two related crystal forms of the same small protein. In both cases, the data look quite decent, and extend beyond 2 A, but the refinement stalls

Re: [ccp4bb] refinement hanging--what am I missing?

that bad, but I share your discomfort. Do the solvent regions retain any significant features? Have you tried flipping those features? Have you applied NCS? What does the Fo - Fc map look like? Charlie On Apr 26, 2013, at 5:38 PM, Patrick Loll wrote: Hi all, Here is a problem that's

Re: [ccp4bb] Advice on img proc software

Bernhard, I've used Matlab to calculate 2D FTs (eg, a Cowtan-esque FT of a cat). I'm sure you could come up with a way to do the phase coloring without too much sweat--the degree of flexibility available to you in this program is quite large. My university has a campus- wide license

Re: [ccp4bb] Help with reducing crystal mosaicity

Jeroen brings up a good point. Back in the old days, around 5 B. C. (Before Cryo), we would use a chilled air generator to blow a stream of cold air along the capillary axis to keep the crystals just above their freezing point--it made a huge difference in crystal lifetime. I recall a

[ccp4bb] MS for verification of protein constructs

I wonder if anyone would care to share experiences/ideas/biases that relate to the use of mass spectrometry to verify the identity of protein constructs used for crystallization. Our experience with different MS facilities has been checquered. Specifically: What's the current thinking

[ccp4bb] coot--saving changes

Posted for my post-doc...for some reason her subscription is slow in starting...any off-line replies should go to [EMAIL PROTECTED] Dear Coot users out there, I am a new coot user and have tried many methods to save changes while rebuilding, short of save coordinates. The manual says

[ccp4bb] SGI monitor on Mac Pro

Hi folks, I just got a new Mac Pro (NVIDIA Quadro FX 4500 graphics card; Apple Cinema LCD display primary) and wonder if I can hook up the big ol' CRT monitor from a now-defunct SGI as my 2nd display. The monitor in question is a 21 SGI/Sony GDM-5411. I have to use two adaptors to

[ccp4bb] ftp server at EMBL?

Does anyone know if the ftp server at EMBL is working? I'm trying to get some of Svergun's SAXS programs, but the ftp connection has just been hanging for the last couple of days... Pat --- Patrick J.

Re: [ccp4bb] apologize

Check out the letters in the Dec 2007 edition of Acta D. There is lively discussion even among the experts (and while I recall no mention of angels in this discussion, there IS a reference to Winnie the Pooh). Acta Cryst. (2007). D63, 1274-1281 Acta Cryst. (2007). D63, 1282-1283 Some

[ccp4bb] radiation damage question

Hi all, I had an interesting experience, and wonder if others have seen similar things. I was collecting data from a crystal that contains an iodinated macromolecule. After 2 days on a copper rotating anode, with the crystal at 100 K, we experienced a detector problem, so I put the

Re: [ccp4bb] helix ordering upon metal binding

Here's an example (although not Fe): Futterer, K., Ravelli, R. B. G., White, S. A., Nicoll, A. J. Allemann, R. K. (2008). Acta Cryst. D64, 264-272. On 8 Apr 2008, at 9:02 AM, Florian Schmitzberger wrote: Dear All, Are there prominent examples of ordering of an alpha-helix within a

[ccp4bb] heavy atom derivative(s) for tutorial

Hi, Does anyone have a foolproof recipe for preparing one or more heavy atom derivatives for a nice, easily crystallized protein like lysozyme? I'm looking for something that I can use as a hands-on MIR/ SIR tutorial for beginning students. I'd rather the students be able to focus their

[ccp4bb] heavy atom tutorial--thanks, and a summary

Thanks to all who responded to my query about cheap, easy, and foolproof systems for teaching students how to do MIR/SAD experiments. Below is a summary of responses. Pat - Summary follows - Jim Pflugrath: Lysozyme

[ccp4bb] ccp4 install on Leopard

Accck! 1. I tried to install Bill Scott's precompiled ccp4 on an intel mac running OS X 10.5. When attempting launch ccp4i, I receive this error message: /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4 /bltwish: no such file or directory Typing which bltwish returns

Re: [ccp4bb] ccp4 install on Leopard

shell you might be using). On Apr 25, 2008, at 1:19 PM, Patrick Loll wrote: Accck! 1. I tried to install Bill Scott's precompiled ccp4 on an intel mac running OS X 10.5. When attempting launch ccp4i, I receive this error message: /sw/share/xtal/ccp4-6.0.2/ccp4i/bin/ccp4i: line 4

[ccp4bb] waaay off topic...

...but I know you'll come through. I'm looking for recommendations for a good textbook covering fluorescence spectroscopy. Thanks in advance. Pat --- Patrick J. Loll, Ph. D.

[ccp4bb] Fwd: [ccp4bb] crystallisation and mosaicity

Hi Charlie, yes you are right, but I assumed if people see a cloud of condensed fog over their LN2 bath they should remove that by a) filling up the bowl completely e.g. some LN2 drips out of the bowl b) blow the fog away before you dip True; this has been demonstrated quite rigorously:

Re: [ccp4bb] Friedel vs Bijvoet

I've always thought that a Bijvoet pair is any pair for which an anomalous difference could be observed. This includes Friedel pairs (h h-bar), but it also includes pairs of the form h h', where h' is symmetry-related to h-bar. Thus Friedel pairs are a subset of all possible Bijvoet

Re: [ccp4bb] Weakest protein-protein complex crystallised

I hope this isn't too much of a foray into philosophy and semantics, but can't you argue that the crystals themselves are weak complexes? And since the energies of crystal contacts are typically very weak, I would further argue that you should be able to crystallize ANY complex with an

[ccp4bb] os x wiki

Does anyone know if the Crystallography on OS X Wiki is down? I haven't been able to access the site for a few days, but I don't know if the site is down, or if some new and insidious stupidness has been perpetrated by the rocket scientists who control IT in our institution...thanks.

[ccp4bb] applied optics--LCD projectors

This is way off-topic, but that's never stopped me before. And what group is better qualified to pontificate about matters lying at the intersection of computers and optics than this one? The LCD projector in our departmental seminar room was stolen over the weekend (!), and I have been

[ccp4bb] pKa for protein C-terminus?

What value do we expect for the pKa of a protein's C-terminal carboxylate? pKa values for free amino acids are quite low (2-3), but it seems to me that this may have something to do with the proximity of a free amine group; I'd expect a higher value (4-ish?) for the peptide's C-terminus.

Re: [ccp4bb] suggestions for UV spectrometer

At the risk of dragging this discussion even further afield from crystallography: How can you get realistic numbers for concentrated solutions using the Nanodrop? I understand that the instrument reduces absorbance by using a very short path length. However, I thought that in order for

[ccp4bb]

Hi all, I just read an appalling article in the science section of today's NY Times that refers to a new magnetic resonance force microscope developed at IBM. The story states For the first time, researchers at an IBM laboratory have captured a three-dimensional image of a virus. Not

Re: [ccp4bb] Crystallography plates, hanging drop but templated sealing film.

This sounds very similar to a nifty little device the folks in Buffalo came up with: J. Appl. Cryst. (1992). 25, 324-325[ doi:10.1107/S0021889891011354 ] HANGMAN: a macromolecular hanging-drop vapor-diffusion technique J. R. Luft and G. T. DeTitta On 15 Jan 2009, at 4:34 PM, Francis E

[ccp4bb] off-topic--refrigerated shakers

Any recommendations for WELL-MADE refrigerated shakers? Our 1980-vintage New Brunswick Psycrotherm* is getting creaky, and the repair people claim that parts are not available. Hence, we're looking at the cost-effectiveness of replacing it with a new one. Probably best to reply off-list,

[ccp4bb] refrigerated shakers, redux

Hi all, Here is a summary of the responses to my inquiry about refrigerated shakers: Virtually all respondents advocated shakers manufactured by New Brunswick Scientific. I have rarely encountered such unanimity in this forum. The only exceptions were three votes for shakers of Swiss

Re: [ccp4bb] Beginning crystallography text

At the risk of appearing immodest: http://www.amazon.com/Protein-Crystallography-Eaton-E-Lattman/dp/0801888069/ref=sr_1_10?ie=UTF8s=booksqid=1278618335sr=1-10 On 8 Jul 2010, at 3:35 PM, Peter Hsu wrote: Hi all, I haven't gotten past the phase of growing the crystal, but I'd certainly

[ccp4bb] waaay off-topic: P-1 pumps

Does anyone know how to disassemble a P-1 peristaltic pump from Pharmacia/Amersham/GE? We have a couple that need simple repairs to either a switch or a rheostat on the control panel, but I'm stumped as to how to actually get the damn thing open. If you've succeeded in doing this, I'd be

Re: [ccp4bb] problem in heavy metal soaking

On 26 Sep 2010, at 9:00 AM, Seema Nath wrote: I'm working with a protein which crystallizes in a mixture of PEG6K with 0.2M AmSO4,my question is if there's any problem if I want to soak heavy metal derivatives in this crystallizing condition? Does AmSO4 interfere in heavy-metal soaking ?

[ccp4bb] tRNA expression

Here's an ignorant question: When people express an exogenous tRNA in E coli (to overcome rare codon issues, for example, or to supply a cognate tRNA for an orthogonal synthetase), what sorts of promoters are used? My (ignorant) guess is that something as potent as the T7 promoter might be a

Re: [ccp4bb] Freezing crystals in a contained system

How low? Back in the old days when we mounted xtals in capillaries, you could sometimes see significant reduction in radiation damage by data collection temperature from room temp to ca. 0 deg C (zero is generally safe, since the PEGS/salts in your mother liquor will depress the freezing

[ccp4bb] xds question: inverse beam, lots of wedges

We've just collected a number of inverse beam data sets. It turns out the crystals showed little radiation damage, so we have a lot of data: 2 x 360 deg for each crystal, broken up into 30 deg wedges. The collection order went like this: 0-30 deg, 180-210, 30-60, 210-240, etc. Now, assuming no

[ccp4bb] MS sequencing of Fab

We've crystallized a complex of an Fab bound to a protein. We have the hybridomas from which the Fab was prepared, but no protein sequence for the antibody. We're trying to plot the easiest course to get the sequence (since the crystals, alas, do not diffract to sufficiently high resolution so

[ccp4bb] off-topic: Small molecule service MS

Can anyone recommend a good fee-for-service facility that does routine high-res mass spec on small molecules? Probably best to reply off-line; and I'd ask you to limit suggestions to facilities within the continental US (for reasons of convenience, rather than chauvinism). Thanks, Pat

Re: [ccp4bb] Protein preps become a jelly

Certainly not unprecedented, or even that unusual (I remember making gels from BSA and IgG solutions during grad school rotations). Gel formation usually requires crosslinking, so consider whether you might be getting adventitious disulfide bond formation. Pat On 30 Aug 2011, at 11:31 AM,

Re: [ccp4bb] Mac OSX 10.7 Lion

Still doesn't beat my all-time favorite, an early Microsoft spell-checker that changed diffract to defrocked. I forgot to mention how delightful the spelling auto-correction feature can be. (It should have read nothing unusual in and of itself). That, at least, can be turned off.

Re: [ccp4bb] Rigaku high voltage tank

Bill, What do you mean by high voltage tank? When I hear this term, I think of the oil- (and PCB-) filled tank housing the transformer on an old generator; but there's nothing like that on the R-Axis. Do you mean the blue box housing the detector controller? If so, then I can tell you that

[ccp4bb] is codon optimization worth it?

Has anyone encountered a case in which a construct with the native sequence expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding construct with a codon-optimized sequence expressed well? (The gene in question is from cerevesiae) Thanks, Pat

Re: [ccp4bb] sealing slides on VDX plates?

Haven't done this for a while, but what we used to do was mix Vaseline plus mineral oil (both purchased for cheap at the local drugstore), and then apply it using a 10 ml syringe with a pipet tip attached. We used the mixture of Vaseline + mineral oil because Vaseline alone is too viscous

[ccp4bb] Beckman Biosys 2000

I was just contacted by a group looking for install disks for the Biosys program used to run the old Biosys2000 FPLC from Beckman. I don't have the install disks anymore (we eventually bludgeoned our Biosys to death, and then set it on fire, if I recall--it was always very unreliable).

[ccp4bb] DDM crystals

Does anyone have any experience with formation of crystals of dodecyl maltoside in the presence of PEG? Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry

[ccp4bb] synchrotron X-ray picture

Hi all, I have a vague memory of having a picture in someone's presentation once, showing a smoking hot X-ray beam emerging from the beam pipe in a hutch at a synchrotron. I think the picture might have been a double exposure, with a long exposure that captured air ionization superimposed on a

[ccp4bb] old-school stereo and Lion

The imminent replacement of Mobile-Me by iCloud provides an impetus for me to upgrade to Lion; but I'm currently happily using old-school stereo (i.e., a CRT monitor + Crystal-Eyes LCD glasses) under Snow Leopard. Can anyone attest to being able to use such equipment with Coot/PyMol under LIon?

Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]

Hear, hear! I'm glad to know I'm not the last grump left standing. When I raise this point every year, my students regard me with bemused stares, as though they've just seen a coelacanth swim past their window... On 1 Apr 2012, at 10:18 AM, Gerard Bricogne wrote: Dear Paul, May I join

[ccp4bb] Postdoctoral position available: Protein recognition of anesthetics

A postdoctoral position will be available Fall 2009 in Philadelphia, PA, USA. The successful candidate will join a collaborative research effort between the Eckenhoff laboratory at the University of Pennsylvania and the Loll laboratory at the Drexel University College of Medicine. This

[ccp4bb] anode lifetime?

Does anyone have a reasonable estimate for the expected working lifetime of a copper anode on a MicroMax007? (Yes, I'm thinking about stimulus funding...). Thanks, Pat --- Patrick J. Loll, Ph. D.

Re: [ccp4bb] phasing with se-met at low resolution

Greg Petsko's group did something like this about a billion years ago (yet, strangely, I remember the paper, even though I'd be stumped if you asked me what I had for breakfast...) They covered the range from room temp down to very cold, using different cryoprotectants (importantly, they

[ccp4bb] coupling between occupancy and b-values in refinement

Hi all, I'm looking for a reference to bolster my response to a referee, in which I defend my decision not to refine the occupancy of a ligand in structure refined at around 2 A resolution (note the ligand binding slte lies on a two-fold crystallographic axis, so the maximum occupancy is

Re: [ccp4bb] TEV nucleotude sequence with restriction site

You seem to be describing the MCS found in many TEV-site-containing expression plasmids (am I missing something?) E.g., look at the sequences in Sheffield et al., Protein Expression and Purification 15, 34 –39 (1999) (let me know if you want a PDF, I don't want to send it to the whole bb)

Re: [ccp4bb] fortran format descriptor help

I get this: read(5,100)xinten,siginten,fobs,sigfobs,itest 100 format(6x,3i5,3(6x,f10.3),/,25x,f10.3,6x,i10) On 17 Jun 2009, at 4:18 PM, Francis E Reyes wrote: INDE 00 -9 IOBS= 9062.000 SIGI= 200.300 FOBS=95.190 SIGMA= 1.060 TEST= 0

Re: [ccp4bb] low UV reading on AKTA prime

I second Scott's post. About the only problem we've had with our Akta instruments is this type of degradation of the filter. I'm not sure what the mechanism is, but the filters do seem to crap out after a while, at least in the cold room (oxidation? I have no idea of what the filter is

[ccp4bb] cheap/useful alternatives to bloatware

Hi, This is off-topic in the sense that it's not about reciprocal space, but graphics ARE an integral part of publishing and teaching... I just upgraded to Leopard*, and find that my versions of Photoshop CorelDraw no longer work. I can't stomach spending big bucks for the new version

[ccp4bb] alternative graphics programs for OS X--summary

Hi, Thanks to the many replies to my queries about cheap/easy alternatives to Photoshop and CorelDraw on OS X. In a rare display of unanimity, the bulletin board spoke with essentially one voice: ALTERNATIVE TO PHOTOSHOP: Gimp (not gimpshop) http://www.gimp.org/ As one sage

Re: [ccp4bb] Sumo protease (Ulp) expression vector

Try PubMed, rather than Google: Weeks SD, Drinker M, Loll PJ (2007) Ligation independent cloning vectors for expression of SUMO fusions. Protein Expr Purif. 2007 May; 53(1):40-50. We express the Ud1 domain of the yeast hydrolase. Contact me off-line if you're interested. Pat On 12

[ccp4bb] off topic--Torrey Pines equipment

Does anyone have any experience with equipment from Torrey Pines Scientific (incubators, constant temperature circulators)? Probably best to reply off-line; if there's a groundswell of interest I can post a summary. Thanks, Pat

[ccp4bb] Postdoctoral position in DUB structural biology

A postdoctoral position is available to study the structures and functions of a novel class of human deubiquitinating enzymes involved in neurodegeneration. An NIH-funded position is available immediately to study the structure, catalytic function, and ligand-binding properties of the

[ccp4bb] Postdoctoral position in anesthetic discovery

We seek a structurally-oriented post-doctoral fellow to participate in a general anesthetic discovery program consisting of high through-put approaches, coupled to medium through-put secondary screens, to include x-ray crystallography, isothermal titration calorimetry and in vivo assays.

[ccp4bb] 3D search for peptide conformers?

I have a 10-residue stretch of a protein that adopts an interesting conformation; I'd like to know if this conformation occurs in other proteins. I'd welcome suggestions for tools that will allow me to to search for this peptide conformation in the PDB. I naturally thought of DALI, but it

[ccp4bb] python install issues?

Hi, I'm simultaneously installing ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard. On both machines, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error:

[ccp4bb] chiral volumes--losing it

Friends, A question about the definition of chiral volumes: I'm looking for the definition of the SIGN of a chiral volume. The only ccp4 reference I can find (readily) is this: http://www.ysbl.york.ac.uk/~garib/refmac/docs/theory/chiral.html This page gives an algorithm for

[ccp4bb] chiral volumes--2nd try

Sorry, the original post looks garbled (mirroring my internal state, no doubt). I'm trying again, sending as plain text: Friends, A question about the definition of chiral volumes: I'm looking for the definition of the SIGN of a chiral volume. The only ccp4 reference I can find (readily)

Re: [ccp4bb] chiral volumes--2nd try

Joel, Agh. I can honestly say that this explanation never occurred to me, even though it is consistent with the data (But come on, any introductory organic chem text explains the R/S rules by moving from atom 2 to 3 to 4, and not by jumping from 2 to 4...surely you would follow the

Re: [ccp4bb] software/web server to determine ligand volume

VOIDOO will do this On 13 Aug 2014, at 2:06 AM, sreetama das wrote: Dear all, Is there any software or web server available to calculate the volume of a ligand if the ligand coordinates are provided? Google seems to come up only with options to calculate protein cavity volume. Thanks in

[ccp4bb] XDS.INP for X25

Hi, I'm trying to help a colleague process some data collected at beamline X25 of the late, lamented NSLS. Does anyone have an XDS.INP file that they know works for such data (this is for the Pilatus detector)? I have kludged together a file that looks right, but the processing still doesn't

[ccp4bb] Off-topic x 2: Chaperone co-expression AND Bac-Mam contract work

Hello everyone, Please allow me to kill two off-topic birds with one email ‘stone’: 1) Can anyone suggest where I can lay hands on the pREP4-GroESL plasmid for bacterial co-expression of GroEL and GroES? I’ve checked with the original author (Philip Cole), but it’s been decades since he

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

How about the ability to compile code? Are there decent compilers readily available for Windows? I like being able to write & compile the occasional fortran program {hic sunt dinosaurs}, and it’s easy to do this on a unix-based platform like OSX. If your reasoned arguments fail, I have found

Re: [ccp4bb] Message from the Uppsala EDS: "Morituri te salutant"

Ave atque vale. The EDS was hugely useful (and will continue to be so in its new manifestation, we hope)—thanks to everyone who made it happen! Pat > On 13 Dec 2016, at 12:51 PM, Gerard DVD Kleywegt > wrote: > > Hi all, > > After tirelessly serving the scientific

Re: [ccp4bb] Crystal with ZERO diffraction

Sadly, I have seen numerous examples of reasonably-sized crystals that give no observable ordered diffraction (I shot a few this weekend, in fact). I can’t give you evidence for what is happening, but I guess that you can build a macroscopic assembly using lattice interactions that are only

[ccp4bb] ample

I’m intrigued by the prospect of using AMPLE to test multiple distant homologs in a MR problem. I’ve used HHPRED to identify about 20 high-probability homologs of known structure, each of which has about 20-25% identity with the unknown protein. However, it’s not clear to me from the

[ccp4bb] comfortable OS X level

I’m still running Yosemite on my Macs, both because I’m change-averse and because folks reported problems with some crystallographic software upon upgrading the OS. These reports have now faded into the haze of the past, and so I ask, have the issues been resolved? Is it safe to move to

Re: [ccp4bb] Fishing crystals from volatile solvent as precipitant

I second (third?) what Tommi and Kevin said about using an oil to cover the drop to slow evaporation (I like paraffin for this—not too viscous). Here’s an additional nuance: Saturate the oil with the alcohol first, before using it to cover the drop. > On 14 Aug 2018, at 2:58 PM, Thomas Krey

Re: [ccp4bb] Unknown density

Calcium likes to form octahedral complexes with water (or other oxygen-containing) ligands. This looks like a classic example. After you model and refine this, you’ll want to check water-metal distances, to make sure they are appropriate for calcium. There is a nice literature on such things,

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

Fig. 2.13 in Gale Rhodes’ “Crystallography Made Crystal Clear” touches on rabbit heads and diffraction, and is one of my favorite cartoons (sadly it doesn’t directly address your problem). > On 2 Nov 2018, at 5:14 PM, Deborah Harrus wrote: > > Dear all, > > I came across an unidentified

Re: [ccp4bb] nonenzymatic removal of His tag?

1) Use a different protease, e.g. SUMO protease, which is sufficiently specific that it’s unlikely to cause any problems even if a little bit is carried along. See, for example (shameless plug #1): DOI: 10.1016/j.pep.2006.12.006 2) Use intein cleavage. NEB sells a vector that lets you fuse an

[ccp4bb] Fwd: [ccp4bb] SO4 or PO4

S has about 0.56 anomalous electrons at 8 keV, whereas P has about 0.44. This is a small difference between two weak signals—unlikely to give a clear result. If you could get to the sulfur & phosphorus edges, then you could (in principle) answer this, but that’s a very hard experiment to

Re: [ccp4bb] A Question about crystal packing

e in this regard. > > Best regard > > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > <https://www.

Re: [ccp4bb] Questionable Ligand Density: 6MO0, 6MO1, 6MO2

The idea of contacting the editor (and/or author) is an excellent one, and indeed the correct thing to do scientifically. However, I’m disillusioned: I’ve been down this path before with a high-profile vanity journal, and while the editors paid lip service to the notion that the record should

Re: [ccp4bb] Space group/Unit cell

This reminds me of something that we crystallized a few years back. It indexed as I222 (or I2(1)2(1)2(1)) and the cell was quite small; too small for the protein of interest. Almost certainly a contaminant, but it didn’t show up in Contaminer. Diffracted like gangbusters, but we never figured

[ccp4bb] CCwork/CCfree

, I mean the peaks of the histograms (phenix.r_factor_statistics suggests R ~ 0.15-0.18, Rfree ~ 0.19-0.22) I realize that I could probably dig up this information on my own, but I’m (feeling lazy)/(desirous of the community’s wisdom). Thanks, Pat Patrick Loll pjl...@gmail.com

[ccp4bb] Fwd: [ccp4bb] AW: Kevin Denkmann lädt Sie zur Zusammenarbeit auf 'Rechnungen' ein.

com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2Fdata=02%7C01%7CHerman.Schreuder%40SANOFI.COM%7Cf86f5afb3c3d4664586e08d87502dc60%7Caca3c8d6aa714e1aa10e03572fc58c0b%7C0%7C0%7C637388002701067474sdata=uu7CmKG9Zpof%2Fid8J%2F66FzB%2ByRkyh6qAdtrkKm8RmEo%3Dreserved=0 >> >> #

[ccp4bb] flow rate for cooling stream?

Sorry, way off topic: Does anyone have an estimate for the flow rate one would typically use for the cold nitrogen stream passing over a protein crystal in a standard data collection? Background: Our nitrogen “generator” has gone belly-up and the vendor no longer services it, so I’m testing

[ccp4bb] dewar horror stories

Hello community, We recently had a dry shipping dewar fail catastrophically (while en route to the beam line, so, major trauma). I sent it to a company that specializes in repair and refurbishing of cryogenic tanks, and they told me it has an internal leak, and hence is not reparable. I was

[ccp4bb] Stabilizing Mitegen reusable bases/mounts

Hi everyone, I’ve become very fond of the Mitegen reusable bases for mounting crystals, since the reusable aspect savse me from having to discard the base every time I break a microloop. However, once the crystals arrive at the synchroteon, I observe motions of the loops (some gradual, some

Re: [ccp4bb] The weekly nonsense

- > Many plausible ideas vanish > at the presence of thought > -- > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4

Re: [ccp4bb] Looking for proteins for undergraduate biochemistry lab

Transglutaminase, also known in some circles as “meat glue." > On 17 Jun 2021, at 11:50 AM, Bryan Lepore wrote: > > Greetings > > This enzyme meets none of the stipulations, but I will point out as it is > somewhat unusual to find in a grocery store : > > A food product called Just Egg

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