Re: [ccp4bb] Crystallizing a tough target

experiments at different temperatures (14C, 21C and 37C), with 37C coming out as the clear winner. best wishes Savvas —— Prof. Savvas Savvides VIB Center for Inflammation Research Ghent University, Dept. of Biochemistry & Microbiology Technologiepark 71, 9052 Ghent, Belgium Email: savvas.s

Re: [ccp4bb] Dry shipper in limbo

andle, drivers and other courier employees actually do remember unusually looking shipments, such as a shipping-case containing a dry-shipper! Best of luck and wishes, Savvas On 28 Jul 2023, at 08:15, Savvas Savvides wrote: Best wishes, Savvas Begin forwarded message: From: "Dr. Ke

Re: [ccp4bb] Structure prediction - waiting to happen

Jane https://doi.org/10.1038/s41592-022-01760-4 A correspondence in Science by Moore, Hendrickson, Henderson and Brunger https://www.science.org/doi/10.1126/science.abn9422?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed Best wishes Savvas ---- Savvas Savv

Re: [ccp4bb] problems with running PARROT

n 25 Jun 2021, at 15:34, Eleanor Dodson wrote: > > The extract from the log file looks OK - can you send the whole log.txt? > Eleanor > > On Fri, 25 Jun 2021 at 12:09, Savvas Savvides <mailto:savvas.savvi...@ugent.be>> wrote: > Dear colleagues, > > I am tryin

[ccp4bb] problems with running PARROT

Dear colleagues, I am trying to run Parrot via CCP4-7.1.014 and the CCP4i2 GUI on a MacBookPro (OSX 10.15.7) and keep getting the following error report as the program is in the process of outputting SigmaA statistics. Below, I provide two pieces of information: (1) The Error message (2) The la

[ccp4bb] Research fellow position at Ghent Un. and the VIB (Ghent, Belgium)

Dear colleagues, please find below a published vacancy for a post-doctoral research fellow in structural biology in our group at Ghent University and the VIB (Ghent, Belgium). For a summary of our research activities please visit: http://www.vib.be/en/research/scientists/Pages/Savvas-Savvides

Re: [ccp4bb] Optimization from needle shaped crystals

Dear Prem, before moving on with any optimization rounds it would be good to first confirm that these crystals are actually protein crystals, and in particular the protein of interest. For example, a Silver-stained SDS-PAGE gel can be very informative. You can run a couple of your crystalline c

Re: [ccp4bb] different residues as alternate occupancy?

The structure of milk proteins obtained from in vivo-grown crystals from a viviparous cockroach could also serve as an interesting case: http://dx.doi.org/10.1107/S2052252516008903 best wishes Savvas > On 24 Jun 2019, at 16:03, Holton, James M >

Re: [ccp4bb] A Max Perutz question

Hey Zac A good scan of page 228 in Georgina Ferry’s biography of Max Perutx (Max Perutz and the secret of life) will do the trick. It is a 18x13 cm photo. I have it in front of me! best Savvas > On 10 Apr 2019, at 16:29, Zachary A. Wood wrote: > > Hello Fellow Structural Enthusiasts, > > My

Re: [ccp4bb] Purchasing slides with diffraction gratings for teaching diffraction

Dear Pietro the ones that I have just used in my lecture are from https://www.patonhawksley.com best wishes Savvas > On 5 Mar 2019, at 10:41, Roversi, Pietro (Dr.) wrote: > > Dear all, > > I'd like to purchase slides with diffraction gratings for educational

[ccp4bb] upcoming VIB conference on Structural Biology

t 10th. On behalf of the organizers, Savvas --- Savvas Savvides VIB Center for Inflammation Research Dept. of Biochemistry & Microbiology, Ghent University Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium +32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: savvas.savv

Re: [ccp4bb] Suggestions for deglycosylaiton enzymes

in combination with enzymatic glycan digestions as described above. Best wishes Savvas --- Savvas Savvides VIB Center for Inflammation Research Dept. Biochemistry & Microbiology, Ghent University Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium +32 (0)472 928 519 (mobile) ; +32 9 331 36

Re: [ccp4bb] His-6 versus His-10 tag

Hi Herman the survey article by Carson in Acta D DOI: 10.1107/S0907444906052024 from a decade ago may provide relevant information/insights. best wishes Savvas > On 19 Sep 2017, at 12:10, herman.schreu...@sanofi.com wrote: > > Dear BB, > > We are

Re: [ccp4bb] CC(1/2) reference

Current Opinion in Structural Biology 2015, 34:60–68 http://dx.doi.org/10.1016/j.sbi.2015.07.003 best wishes Savvas Savvas Savvides VIB-UGent Center for Inflammation Research Dept. Biochemistry & Microbiology, Ghent University Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium +3

Re: [ccp4bb] A question about Cys and fluoro benzene ring

). This would even tell you if the particular cysteine in your structure is truly the relevant covalent target. In this way you can even compare washed and dissolved crystals of your protein-ligand complex with the complex in solution. best wishes Savvas --- Savvas Savvides VIB-UGent Center for

Re: [ccp4bb] Glycoprotein expression question

Dear Bernhard Our campaigns over the years aiming to produce mammalian cytokines and the ectodomains of cytokine receptors via eukaryotic expression systems (mainly in several HEK293 flavors) for structural biology, have taught us that the N-linked glycosylation issue remains a very empirical ex

[ccp4bb] post-doctoral position at VIB-Plant Systems Biology, Belgium.

structural biology groups within the VIB institute (Savvas Savvides, VIB/UGent and Rouslan Efremov, VIB/VUB). The successful candidate will spearhead the structural elucidation of an enigmatic endocytic complex and will become part of a lively research group with a long track record on unravelling

Re: [ccp4bb] MR phasing using Negative Stain EM reconstruction

rovide additional options as well. http://journals.iucr.org/j/issues/2016/03/00/ap5002/ap5002.pdf <http://journals.iucr.org/j/issues/2016/03/00/ap5002/ap5002.pdf> best wishes Savvas Savvas Savvides Ghent University, L-ProBE VIB Inflammation Research Center (IRC) Technology Park 927,

Re: [ccp4bb] additional density on cysteine residue

increased beyond the modeled S-OH group after refinement and the features thereof, provide evidence for the likelihood of a mixed-disulfide with betaME. best wishes Savvas Savvas Savvides Unit for Structural Biology, L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS

Re: [ccp4bb] Space group problem?

Dear Chen, how sure are you that your crystals contain the protein of interest? Repeatedly washing harversted crystals in crystal stabilization solution followed by SDS-PAGE coupled to appropriate staining protocols (e.g. Coomassie, Silver staining) or western blotting can give a pretty conclus

[ccp4bb] university-funded research position in structural biology at Ghent University, Belgium

Dear colleagues, I have taken the liberty of drawing your attention to a university-funded post-doctoral position in structural biology that is currently available at the Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University (Belgium). The succesful candida

[ccp4bb]

Savvas Savvas Savvides Unit for Structural Biology, L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS/texting +32 (0)472 928 519 Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html On 19 Mar 2014, at 16:58, Yarrow Madrona wrote: > Thank you

Re: [ccp4bb] N-linked glycans mediate inter-molecular protein-protein interactions

Dear Tianyu, I have found the recent review by: Nagae and Yamaguchi in Int. J. Mol. Sci. 2012, 13, 8398-8429; doi:10.3390/ijms13078398 quite a good starting point. best Savvas On 05 Feb 2014, at 19:53, Gmail wrote: > Dear colleagues, I am looking for structures of protein complexes in which

Re: [ccp4bb] Puzzling Structure

i meant to say P21212 On 12 Apr 2013, at 21:47, Savvas Savvides wrote: > The CRYST1 in the pdb header is problematic. > CRYST1 95.520 47.815 88.570 90.00 90.00 90.00 P 21 21 218 > it looks like the number '1' was paired to the space group rather than the >

Re: [ccp4bb] Puzzling Structure

The CRYST1 in the pdb header is problematic. CRYST1 95.520 47.815 88.570 90.00 90.00 90.00 P 21 21 218 it looks like the number '1' was paired to the space group rather than the space grop number (i.e. nr. 18 for P21212) Table 1 in the paper specifies P212121 as the space group.

Re: [ccp4bb] refinement protein structure

necessary food for thought to proceed. Very best wishes Savvas Savvas Savvides Unit for Structural Biology, L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS/texting +32 (0)472 928 519 Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html On 27

Re: [ccp4bb] FW: [ccp4bb] [ccp4bb] disulfide engineering

We have had some good luck with hydrogen peroxide [for technical details plus validation via a crystal structure see Van der Meeren et al JBC 288(2):1214-1225, (2013)]. best of luck Savvas On 28 Feb 2013, at 12:14, "McEwan, Paul" wrote: > Rather than looking at “anti-DTT” it is more import

Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!

Hi Jacob, check out Figure 1 in Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser. Redecke L, et al. Science. 2013 Jan 11;339(6116):227-30. and In vivo protein crystallization opens new routes in structural biology. Koopmann R. Nature Methods. 2012

Re: [ccp4bb] S-nitrosylation protein

Dear Uma, A very complehensive survey of the state-of-the-art in this topic can be found in the following literature resources: (1) Garman EF. Radiation damage in macromolecular crystallography: what is it and why should we care? Acta Crystallogr D Biol Crystallogr. 2010 Apr;66(Pt 4):339-51.

Re: [ccp4bb] a challenge

Dear James > I actually chose 3dko because it is a kinase (with a ligand), and > therefore an interesting candidate for a molecular replacement > "score". I have not set this up yet, but I think if you look for PDB > entries that contain the word "kinase" and try to molecular-replace > all of the

Re: [ccp4bb] estimate of effective concentration

/nature10183 best regards Savvas Savvas Savvides Unit for Structural Biology, L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Tel/SMS/texting +32 (0)472 928 519 Skype: savvas.savvides_skype http://www.LProBE.ugent.be/xray.html On 21 Jun 2012, at 01:08, Filip Van Petegem

Re: [ccp4bb] help regarding structure solution

Dear Sonali have you run any diagnostics on your dataset e.g. via xtriage in PHENIX, or the ccp4 programs to detect issues such as twinning and pseudotranslation. You also did not provide any information regarding the data quality. Processing your dataset via Xia2 from the ccp4 suite could also

Re: [ccp4bb] Do my SAXS data agree with the crystal structure?

It might also be useful to go through the recent paper by Jacques et al Acta cryst D68:620-6 (2012) towards the standardization of saxs data analysis, diagnostics and reporting. Best regards, Savvas On 17-jun.-2012, at 13:01, David Briggs wrote: > Dear Xun, > > Regarding your monomer v

Re: [ccp4bb] CSX

Dear Uma Your modeling of a Cysteine sulfenic group (SOH) is reasonable given the observed difference density but do keep in mind that sulfenic groups are very susceptible to further oxidation to sulfinic and sulfonic acids. Stabilization of sulfenic and sulfinic groups in enzyme active sites is

Re: [ccp4bb] Suggestions for solving a structure with 8-10 copies per asymmetric unit

Dear Jiyuan have you run any data diagnostics on your dataset? Ccp4 offers quite some options (truncate, detwin etc), and xtriage from PHENIX is also very powerful. And how sure are you of your laue group symmetry and space group (pointless via ccp4 and xtriage via PHENIX can be very helpful)? A

Re: [ccp4bb] Aggregated protein for crystallization

Dear Raji Running a blue-native gel with lanes in the presence and absence of a reducing agent could prove quite informative. DLS could also return a quick result on the particle distribution in your sample. In that case I would measure samples as fractionated from the superdex200 and compare th

Re: [ccp4bb] mutagenesis based on ligand-bound crystal structures

Dear Chris A whole series of studies from the early to late 90's did his for the growth hormone-GHR interaction. Papers by Pearce, Cunningham, Clackson and Wells come to mind. Also a recent study on the IL13-IL13R interaction by Lupardus et al has covered most of the interaction epitope. Best

Re: [ccp4bb] Freezing crystal

Dear Theresa Cryo-cooling the crystals straight out of their drops or after brief incubations in crystal stabilization solutions containing >2M ammonium sulfate may be the way to go. Here is a copy/paste piece from Kyndt et al (2007) Biochemistry 46, 95-105. All the best Savvas Aliquots (0.5 í L

Re: [ccp4bb] model building at 3.2 A

Dear Kumar Could you please provide some information on your refinement protocol/progress and quality of your partial model thus far. Also, what is the quality and completeness of your data, in particular in the lowest resolution to 10 angs range. In this way one might be able to provide more

Re: [ccp4bb] Movements of domains

Dear Filip 'Annoying' MR problems for which the answer often lies in relatively small differences between the search model and 'RB-shifted' domains and/or subdomains in the actual structure, are I think a good experimental indication of the significance of such issues. To extrapolate from this,

Re: [ccp4bb] effect of Izit dye within the crystal structure

Dear Adam and colleagues The enzyme human glutathione reductase (hGR) binds dyes such as safranin and xanthene, which are analogous to methylene blue (aka IZIT) with respect to their heterocyclic ring structures, in a cavity deep at the dimer interface. Safranin and xanthene are also inhibitors

Re: [ccp4bb] Parrot NCS averaging

Dear Herman In some cases density modification starting with MR phases can indeed prove very powerful. We recently used Parrot to bootstrap a difficult case at 4.3 angs and were able to obtain very good maps for entire missing domains. See Supplementary Fig 1 in:Verstraete et al 2011 BLOOD 118:

Re: [ccp4bb] crystals sticks to the plate surface

Der Atul this topic was previously summarized on the ccp4wiki http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Sticky_crystals best Savvas On 02 Sep 2011, at 08:00, atul kumar wrote: > hi all > > I have crystals which have tendency to stick with the plate and while i try > to pick

Re: [ccp4bb] Methods for dehydrating crystals

Dear Andrea check out: Post-crystallization treatments for improving diffraction quality of protein crystals. Heras B, Martin JL. Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1173-80. All the best Savvas On 26 Aug 2011, at 22:53, Andrea L Edwards wrote: > Hi all, > > What are the mos

Re: [ccp4bb] spherulites and PEG3350

Dear Jan I would recommend running the following protocol on your spherulites. Just pretend that they are crystals :) This was posted some time ago on the ccp4bb. best regards Savvas > On Tue, Nov 2, 2010 at 9:15 AM, Kenneth Verstraete < > kenneth.verstra...@ugent.be> wrote: > > > Hi Ivan, > > >

Re: [ccp4bb] FW: [ccp4bb] highly glycosylated protein

The HEK293S/ I-/- strain (Reeves et al PNAS 2002) does not lack glycosylation capacity. It is deficient in a key glucosyl transferase responsible for adding glycans beyond the Man5GlcNac2. This produces N-linked glycosylated proteins with homogeneous glycan trees. We recently established stabl

Re: [ccp4bb] off topic: problematic protein

I would like to thank all of you who promptly replied to my posting with so many ideas and suggestions (18 answers so far). I will post a summary soon. best wishes to all Savvas >> >> >> On Apr 19, 2011, at 12:48 PM, Savvas Savvides wrote: >> >>> Dear coll

[ccp4bb] off topic: problematic protein

pping' effect. Interestingly, the protein has a calculated pI of 3.5 ! As the options for handling this protein are indeed quite numerous, we would be grateful for any additional input and possible tips/tricks. I will prompty post a summary of the thread. Best regards Savvas et al. -

Re: [ccp4bb] Off topic: How to identify a unknown ligand

Hi Xiaopeng To add to Artem's comments: Does the presumed gsh make a mixed disulfide in the active site?i.e. is it covalently bonded to the active site via a s-s bond? If yes then MS on your purified sample should easily give you the answer. If a mixed s-s is indeed the scenario then purifying the

Re: [ccp4bb] Crosslinking of Protein-Protein complex for crystallisation

Dear Catrine can you comment on the pH range of your crystallization hits compared to the pH of the sample you use for your crystallization trials? The pH can be a major issue depending on the nature of the interaction interface. best regards Savvas On 14 Mar 2011, at 13:21, Catrine Berth

Re: [ccp4bb] How to crystallize a helicase

I would certainly try cocrystallizing with adp, amppnp, or ATPgS Many helicases have been crystallized in this way. Papers by Sawaya et al and Singleton et al come readily to mind. Best of luck Savvas On 09 Mar 2011, at 15:52, Ed Pozharski wrote: > On Wed, 2011-03-09 at 10:52 +, Art wro

Re: [ccp4bb] optimization of dumbbell like crystal

Dear Harvey Based on the experimental history you provided I would try two quick things in order to obtain additional dimensions for your condition. (1) set up your best consensus condition against an additive screen (e.g. From Hampton). (2) I would repeat your last pH vs precipitant grid agai

Re: [ccp4bb] Detaching crystals from glass cover slides

Dear Wataru check out the following entry on the CCP4-wiki on 'sticky crystals' which we compiled based on feeback from many crystallographers: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Sticky_crystals Best regards Savvas ---- Savvas Savvides Unit for Structural B

Re: [ccp4bb] Strange density on Serine oxygen.

it turns out to fit the density very well. I will have > the protein sequenced again to see if it is wrong sequece or O-linked > glycosylation. > > I'll let you know if it turns out to be O-linked glycosylation. > > All the best, > > Vinson > 发件人： Savv

Re: [ccp4bb] Strange density on Serine oxygen.

system that processes the protein in that way. Ser/Thr tandems are well known targets for O-glycosylation (http://www.cbs.dtu.dk/databases/OGLYCBASE/). best regards Savvas Savvas Savvides Unit for Structural Biology @ L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Ph

Re: [ccp4bb] High Rmerge with thin frames

to be refined even more, see Optimization. Best regards Savvas Savvas Savvides Unit for Structural Biology @ L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Ph. +32 (0)472 928 519 http://www.LProBE.ugent.be/xray.html On 05 Nov 2010, at 09:40, Sergei Strelkov wrote

Re: [ccp4bb] offtopic: effect of compound impurities on ITC?

E. Isothermal titration calorimetry to determine association constants for high-affinity ligands Nat Protoc. 2006;1(1):186-91. Best regards Savvas Savvas Savvides Unit for Structural Biology @ L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Ph. +32 (0)472 928 519

Re: [ccp4bb] DLS

Hi Wojtek I can easily second Dave's comment! Best Savvas Savvas Savvides Unit for Structural Biology @ L-ProBE Ghent University K.L. Ledeganckstraat 35, 9000 Ghent, Belgium Ph. +32 (0)472 928 519 http://www.LProBE.ugent.be/xray.html On 04/02/10 14:54, "David Briggs"

Re: [ccp4bb] Solubilization buffer

solubilization of their inclusion bodies for refolding protocols. best wishes Savvas Savvas Savvides http://www.lprobe.ugent.be/xray.html -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Joerg Standfuss Sent: Thursday, December 03, 2009 8:57 AM

Re: [ccp4bb] Phase separation to crystals

Hi James, just out of curiosity. Did IZIT convincingly color the crystals? We have recently seen that crystals grown in high concentrations of MPD do not color with IZIT. This phenomenon was documented in Eckert et al. Acta Cryst. (2003). D59, 139-141. Best regards Savvas Savvas

Re: [ccp4bb] Cryoprotection in > 3M ammonium sulfate

iption of what we did. Best of luck Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: savvas.savvi...@ugent.be http://www.lprobe.ugent.be/xray.html

Re: [ccp4bb] cyseteine modification

environment to remain stable. See for example some previous work of ours on sulfenic and sulfinic forms of active-site cysteines in glutathione reductase (Nature Structure Biology vol 5, 267-271, 1998) and the corrresponding pdb entries 1dnc and 1gsn. Best regards Savvas Savvas Savvides L

Re: [ccp4bb] heavy atom derivative choice

Hi Sebastiano, Given that your crystallization condition contains KSCN, I would certainly give Hg(SCN)2 a go among other Hg options for a protein containing free cysteines. Hg(SCN)2 might end up being more compatible with your crystal form, and might thus minimize non-isomorphism issues. Best of

Re: [ccp4bb] unknown density

- Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 http://www.lprobe.ugent.be/xray.html -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk

Re: [ccp4bb] multi-domain protein with identical tertiary structure

Hi Shankar gamma-crystallin is likely a good candidate [Blundell et al. Nature 289:771-777, 1981], and it in fact goes a step further. It combines two nearly identical greek-key motifs in each domain, which are then connected via a loop to make a dimer. This is all in one chain. Best wishes Sa

Re: [ccp4bb] Halide soaking

histidines had also been iodinated! In retrospect, I had actually run across those peaks in my cross-difference fourier maps but thought that they were too 'secondary' to be included in the heavy atom model. Best wishes Savas ---- Savvas Savvides L-ProBE, Unit for Structural Biology Ghent

Re: [ccp4bb] Se oxidation

wishes Savvas Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: savvas.savvi...@ugent.be http://www.lprobe.ugent.be/xray.html From: CCP4

[ccp4bb] 'Sticky Crystals' on ccp4-wiki

hes Savvas ---- Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghent, BELGIUM office: +32-(0)9-264.51.24 ; mobile: +32-(0)472-92.85.19 Email: savvas.savvi...@ugent.be http://www.lprobe.ugent.be/xray.html E-mail message checked by Spyw

[ccp4bb] SUMMARY: Sticky crystals

Dear colleagues, I would like to thank all of you who responded so generously (either privately or publically on the ccp4bb) to my question on how to deal with 'sticky crystals'. I provide below a consensus of all the many answers grouped according to the proposed solution. Best wishes Savvas

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

Hi Fred, I am not sure if this has been brought up already. Another possibility might be to generously pipet your Ni- or Co-matrix of choice directly to buffered solubilized inclusion bodies, incubate for some time (even overnight if you feel its necessary), and then use the slurry to pack a column

[ccp4bb] sticky crystals

e the most out of the crystals we have grown thus far. We would therefore very much appreciate any input/ideas on manipulating these crystals for data collection. Best wishes Savvas ---- Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35

Re: [ccp4bb] Crystals grown from high ammonium sulphate

atone indicated that only crystals flash-cooled by plunging them directly from their native drops into liquid nitrogen produced diffraction of acceptable quality." Best wishes Savvas ---- Savvas Savvides L-ProBE, Unit for Structural Biology Ghent University K.L. Ledeganckstraat 35 9000 Ghen

Re: [ccp4bb] birefringent spacegroups

Hi Jacob, Chek out Section 2 in the following paper: Echalier et al. (2004) Assessing crystallization droplets uding birefringence. Acta Cryst D60, 696-702. It offers a very effective summary of the physical basis of crystal birefringence and reiterates the classification of crystal optics based

Re: [ccp4bb] phenix.refine and refmac

Hi Yang how many reflections do you have in your test-set for calculating R-free? Too few reflections, typically less than 500, may not constitute a statistically robust cross-validation data set, and thus may lead to fluctuations in R-free plus a tendency for R-free to increase as a function of

Re: [ccp4bb] wich program to test an alternative phaser solution

Hi Fred, in future PHASER runs you can also ask the program to write out an X number of the top solutions as separate coordinate files via the keyword TOPFILES (e.g 'TOPFILES 10' for the top ten solutions). In the PHASER GUI you can enter that request in the 'Define Data' block. best wishes, Savva

Re: [ccp4bb] His tag on membrane protein

Hi Deliang, My own experience with two membrane proteins suggests that His-tag issues pertaining to soluble proteins also seem to apply to membrane proteins. In one case, for example, cleaving the N-terminal His-tag improved the solubility of the protein dramatically. Interestingly, expre

Re: [ccp4bb] Flexible proline?

Hi Tiancen, provided that you know for sure that your Gly->Pro mutation has been incorporated (see Artem's comment) I would spend some more time modeling your Pro. Here are some things to consider: (1) If the view of the model you provided has not fooled me, I believe that the main-chain

Re: [ccp4bb] Solvent content of membrane protein crystals

fice: (517) 355-9724 Lab: (517) 353-9125 FAX: (517) 353-9334Email: [EMAIL PROTECTED] On Sep 24, 2007, at 2:29 AM, Tommi Kajander wrote: Quoting Edward Berry <[EMAIL PROTECTED]>: Savvas Savvides wrote: Indee

Re: [ccp4bb] Solvent content of membrane protein crystals

solvent. In some cases I think waters should be included in the model not solvent- say for structural waters buried in the protein at least. Ed Savvas Savvides wrote: Dear colleagues, in estimating the solvent content of membrane protein crystals it would only seem reasonable that micelle si

[ccp4bb] Solvent content of membrane protein crystals

Dear colleagues, in estimating the solvent content of membrane protein crystals it would only seem reasonable that micelle size should also be taken into account. Depending on the aggregation number and MW of a given detergent, the concentation of detergent used, and the buffer conditions

Re: [ccp4bb] the worst molecular replacment probes

The paper below can put things in perspective a little bit. Bernstein and Hol (1997) Acta Crystallogr D Biol Crystallogr. 53(Pt 6):756-64. Probing the limits of the molecular replacement method: the case of Trypanosoma brucei phosphoglycerate kinase. best wishes Savvas

[ccp4bb] pseudo-translation vectors in molrep vs other programs

Dear colleagues, I would like to thank J. Murray, J. Wright, K. Futterer, E. Dodson, A. Forster, and F. Long for responding to my posting of two days ago on pseudo-translation vectors in molrep vs other programs (see original posting at the end of this message). I should have said at the outset tha

[ccp4bb] pseudo-translation vector in molrep

Dear colleagues, For a particular MR problem I am dealing with, 'analyse_mr' suggests that there maybe a pseudo-translation vector as evidenced by the very significant non-origin peaks in the native patterson: e.g GRID 80 112 80 CELL 104.8290 151.2840 109.4910 90. 118.1310 90. A

Re: [ccp4bb] /usr/lib/libGL.so.1: no version information available

Dear Paul, thanks for confirming that this is a benign remark from Coot. In the meantime, I got replies from other users who are seeing the same thing on their systems. best regards Savvas Quoting Paul Emsley <[EMAIL PROTECTED]>: On Fri, 2007-06-01 at 14:35 +0200, Savvas Savvides

[ccp4bb] /usr/lib/libGL.so.1: in Coot

Dear CCP4 users and developers, upon starting up Coot-0.3.1 as distributed in the CCP4_v6.0.2 binaries for Red Hat 8 we get the following: current_exe_dir is /usr/local/CCP4_v6.0.2/Coot-0.3.1/bin COOT_PREFIX is /usr/local/CCP4_v6.0.2/Coot-0.3.1 /usr/local/CCP4_v6.0.2/Coot-0.3.1/bin/coot-real: /usr

Re: [ccp4bb] Crystallisation of a extremly soluble protein

Hi Sabine, I vaguely recall that an old colleague had used a mini detergent screen (as additive) to solve a problem such as yours. It may be worth setting up a plate or two to screen a few conditions before you embark into more molbio. You can use the 96 well plates with multiple wells (Corning sel

Re: [ccp4bb] Fancy crystal, poor diffraction

Dear Tiancen, for a survey of post-crystallization options, I highly recommend the following review article: Heras B, Martin JL. 2005 Post-crystallization treatments for improving diffraction quality of protein crystals. Acta Crystallogr D Biol Crystallogr. 61, 1173-80. best of luck Savvas Qu