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_id=ori:rid:crossref.org_dat=cr_pub%20%200pubmed Best wishes Savvas Savvas Savvides VIB Center

Re: [ccp4bb] problems with running PARROT

021, 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 trying to

[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

[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

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, > >

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.savvides_

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

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

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

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

with 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

[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

[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 amadr...@uci.edu wrote

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 adams.wan...@gmail.com wrote: Dear colleagues, I am looking for structures of

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] Puzzling Structure

i meant to say P21212 On 12 Apr 2013, at 21:47, Savvas Savvides savvas.savvi...@ugent.be 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

Re: [ccp4bb] refinement protein structure

)) will provide the 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

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 paul.mce...@evotec.com wrote: Rather than looking at

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.

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 them into

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 drdavidcbri...@gmail.com wrote: Dear Xun,

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

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)?

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

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.

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

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

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

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

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 most

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, there

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

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 colleagues We are working on a large bacterial

[ccp4bb] off topic: problematic protein

' 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. Savvas

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

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

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 epozh...@umaryland.edu wrote: On Wed, 2011-03-09

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

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 Biology @ L

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] Strange density on Serine oxygen.

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： Savvas Savvides savvas.savvi...@ugent.be 收件人： Vinson LIANG lwg_conrad_1

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 drdavidcbri

Re: [ccp4bb] Solubilization buffer

to 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] 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] Cryoprotection in 3M ammonium sulfate

. 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 -Original Message

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

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 University

[ccp4bb] 'Sticky Crystals' on ccp4-wiki

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 Spyware Doctor

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

[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

[ccp4bb] sticky crystals

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 9000

Re: [ccp4bb] Crystals grown from high ammonium sulphate

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 Ghent, BELGIUM

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

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,

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,

[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

[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

[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.