Re: [ccp4bb] R: [ccp4bb] Heavy atom vs light atoms density

[Jrh Gmail]

Dear Vito
I looked at the examples of I3C in 3e3d, 3e3s and 3e3t and certainly the latter 
two show clear 2Fo-Fc for several I3Cs at a range of occupancies. So my mention 
of the different difference maps’ effectiveness does not apply. 
Hermann and Eleanor suggestions hopefully will explain your I3C map visibility 
you showed
Best wishes
John 

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 



> On 10 Jun 2020, at 09:39, John R Helliwell  wrote:
> 
> Dear Vito,
> The I3C isn't like the platins as a challenge to the 2Fo-Fc map.
> It maybe is more akin to the situation we described here:-
> https://onlinelibrary.wiley.com/doi/abs/10.1107/S0907444903004219
> ie what does your Fo-Fc map, with three iodines placed, at the correct 
> occupancy, look like? 
> Best wishes,
> John 
> 
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
>>> On 10 Jun 2020, at 09:34, Vito Calderone  wrote:
>>> 
>> Dear Pierre,
>> I was in particular talking of 2FoFc refinement maps.
>> In the attached picture for example you can see the 2FoFc map contoured at 1
>> sigma level of an I3C molecule bound to a protein where for I3C the only
>> visible density is that of iodines whereas the density of the other atoms of
>> the ligand is insignificant.
>> Best regards
>> 
>> Vito
>> 
>> -Messaggio originale-
>> Da: CCP4 bulletin board  Per conto di LEGRAND Pierre
>> Inviato: mercoledì 10 giugno 2020 09:31
>> A: CCP4BB@JISCMAIL.AC.UK
>> Oggetto: Re: [ccp4bb] Heavy atom vs light atoms density
>> 
>> Dear Vito,
>> Could you precise in what kind of maps are you experiencing these effects:
>> 2FoFc refinement maps or experimental phasing ?
>> I had this kind of effects long ago in experiemental phasing due to Fourier
>> transform ripple effects. This could be due to scaling problems, low
>> resolution truncation or incompletness (maybe intensity overloads).
>> Another source condition could be local X-ray dose degradation due to the
>> high absoption of the metals.
>> Best regards,
>> Pierre Legrand
>> PROXIMA-1, SOLEIL
>> 
>> De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Vito
>> Calderone [calder...@cerm.unifi.it] Envoyé : mercredi 10 juin 2020 08:42 À :
>> CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Heavy atom vs light atoms density
>> 
>> Dear All,
>>   many of us have probably experienced that, in the diffraction
>> of protein ligands containing heavy atoms (cisPt, I3C, etc), the
>> overwhelming electron density of the metal can totally flatten that of the
>> light atoms around (or rather make it look insignificant).
>> Is anyone aware of an article/review (to use as a reference) in which this
>> is clearly stated/pointed out?
>> Best regards
>> 
>> Vito Calderone
>> 
>> 
>> 
>> 
>> 
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Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

[Jrh Gmail]

Dear Michael
The Rmerge in the strong intensity bin of 0.079 is untypically high it seems to 
me. 
Were the diffraction images underexposed? 
Best wishes
John

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 



> On 3 Nov 2019, at 23:19, Michael Jarva  wrote:
> 
> 
> Hi CCP4BB,
> 
> I have some unusual crystal diffraction data I'd like to get your input on.
> 
> Almost a year ago I shot some small rods sticking out of a loop, so basically 
> no liquid around them - using the microfocus MX2 beamline at the australian 
> synchrotron, collected on an EIGER 16M detector.
> 
> The crystals diffracted weakly and was seemingly not viable at first glance 
> because of high Rmerge/Rpims. See the aimless summary at the bottom of this 
> post. This seemed to stem from a low spot intensity at low resolutions 
> (I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.
> 
> Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 
> 8.02 Å^2.
> 
> Density maps looked great and the build refined easily enough (R/Rfree 
> 0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is 
> lower than any other structure deposited in that resolution bin. Furthermore, 
> the molprobity score is 0.83, and overall real-space correlation CC is 0.855.
> 
> So my question is, can I feel comfortable depositing this? 
> 
> best regards
> Michael
> 
> Chosen Solution:space group P 1 21 1
> Unit cell:44.93   41.90   45.83  90.00  115.57   90.00
> Number of batches in file:   1659
> The data do not appear to be twinned, from the L-test
> Overall InnerShell OuterShell
> Low resolution limit   41.34 41.34  2.49
> High resolution limit   2.40  8.98  2.40
> 
> Rmerge  (within I+/I-) 0.231 0.084 0.782
> Rmerge  (all I+ and I-)0.266 0.099 0.983
> Rmeas (within I+/I-)   0.323 0.118 1.091
> Rmeas (all I+ & I-)0.317 0.118 1.167
> Rpim (within I+/I-)0.225 0.084 0.759
> Rpim (all I+ & I-) 0.171 0.063 0.623
> Rmerge in top intensity bin0.079- - 
> Total number of observations   19901   362  2067
> Total number unique 6054   126   611
> Mean((I)/sd(I))  2.7   4.6   1.0
> Mn(I) half-set correlation CC(1/2) 0.958 0.991 0.570
> Completeness98.6  98.2  97.3
> Multiplicity 3.3   2.9   3.4
> Mean(Chi^2) 0.48  0.33  0.50
> 
> Anomalous completeness  81.7  92.2  75.1
> Anomalous multiplicity   1.5   1.8   1.9
> DelAnom correlation between half-sets -0.003 0.041 0.045
> Mid-Slope of Anom Normal Probability   0.704   - -  
> 
> The anomalous signal appears to be weak so anomalous flag was left OFF
> 
> Estimates of resolution limits: overall
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.67A 
>from Mn(I/sd) >  2.00: limit =  2.87A 
> 
> Estimates of resolution limits in reciprocal lattice directions:
>   Along0.96 a* - 0.28 c*
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.40A  == maximum 
> resolution
>   Along k axis
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.86A 
>   Along   -0.17 a* + 0.99 c*
>from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum 
> resolution
>from Mn(I/sd) >  1.50: limit =  2.98A 
> 
> Anisotropic deltaB (i.e. range of principal components), A^2:  8.62
> 
> Average unit cell:44.93   41.90   45.83   90.00  115.57   90.00
> Space group: P 1 21 1
> Average mosaicity:   0.05
> 
> Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   
> 0.00   0.00
> 
> 
> 
> 
> Michael Jarva, PhD
> ACRF Chemical Biology Division
> The Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade
> Parkville Victoria 3052
> Australia
> Phone: +61 3 9345 2493 
> Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/
> The ACRF Chemical Biology Division is supported by the
> Australian Cancer Research Foundation
> 
> ___ 
> 
> The information in this email is confidential and intended solely for the 
> addressee.
> You must not disclose, forward, print or use it without the permission of the 
> sender.
> 
> The Walter and Eliza Hall Institute 

Re: [ccp4bb] tNCS incompatible with cell dimensions

[Jrh Gmail]

Dear Kevin
You could try reindexing into P1, then run Phaser and with its solution as 
input to Zanuda determine the space group. 
Best wishes,
John 

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 




> On 31 May 2019, at 21:09, Kevin Jude  wrote:
> 
> Hello community, I wonder if I could solicit advice about a problematic 
> dataset. I plan to solve the structure by molecular replacement and expect 
> that the protein is relatively compact, ie not elongated. SAXS data supports 
> this expectation.
> 
> The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2 with 
> a = 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with 40% 
> solvent. The native Patterson shows a large peak (12 sigma) suggesting a tNCS 
> vector of {0.5, 0.5, 0}.
> 
> If you're sharper than me, you may have already spotted the problem - c is 
> the long axis of the unit cell, but tNCS constrains the proteins to a plane 
> parallel to the a,b plane. Indeed, molecular replacement attempts using 
> Phaser will not give a solution in any orthorhombic space group unless I turn 
> off packing, and then I get large overlaps in the a,b plane and huge gaps 
> along c.
> 
> Since I believe that my model is good (or at least the correct shape, based 
> on SAXS), I wonder if I'm misinterpreting my crystallographic data. Any 
> insights into how to approach this problem would be much appreciated.
> 
> --
> Kevin Jude, PhD
> Structural Biology Research Specialist, Garcia Lab
> Howard Hughes Medical Institute
> Stanford University School of Medicine
> Beckman B177, 279 Campus Drive, Stanford CA 94305
> Phone: (650) 723-6431
> 
> 
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[ccp4bb] UK Open Research Data Task Force Final Report

[Jrh Gmail]

Dear Colleagues 
The UK Open Research Data Task Force Final Report is here:-
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/775006/Realising-the-potential-ORDTF-July-2018.pdf
 
This will be of general interest. As well as contributing to this report I 
wrote the crystallography case study. 
Best wishes, 
John 

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 
Chairman of IUCr Committee on Data





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Re: [ccp4bb] FW: [ccp4bb] old data - headers

[Jrh Gmail]

Hello Harry
I used SRS 7.2 and 9.6 at a wide variety of monochromatic wavelengths for 
resonant scattering (AD) studies. But I can imagine high intensity application 
PX measurements were made at those specific wavelengths which you mention.
Greetings from Novosibirsk,
John 

Emeritus Professor of Chemistry John R Helliwell DSc_Physics 




> On 31 Jan 2019, at 18:02, Harry Powell 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> This looks like it was on beamline 7.2 (which had a fixed wavelength of 
> 1.488Å, according to an article written by Liz Duke - see 
> https://www.ccp4.ac.uk/newsletters/newsletter37/11_beamline14.html); I can't 
> remember if detector 421 was a Q4 or a Q4R, but (again, according to the same 
> article) Daresbury certainly had at least one of each at some time!
> 
> BL 7.2 was actually the only beamline at Daresbury that I collected my own 
> data on (before I worked on Mosflm) - using an Arndt-Wonacott camera and 
> film...
> 
> Harry
> 
>> On 31 Jan 2019, at 10:48, Dean Derbyshire wrote:
>> 
>> huge thanks everyone.. what a response.  All good now
>> :)
>> 
>> 
>> -Original Message-
>> From: Pedro Matias [mailto:mat...@itqb.unl.pt] 
>> Sent: den 31 januari 2019 11:46
>> To: Dean Derbyshire ; CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] FW: [ccp4bb] old data - headers
>> 
>> Hi Dean,
>> 
>> I reckon that it is an ADSC Quantum 4 or 4R CCD detector. If you open the 
>> images with mosflm or adxv you should see the characteristic 2x2 tile 
>> pattern.
>> 
>> Note how the header format is similar to the one you posted from the ESRF.
>> 
>> Pedro
>> 
>> Às 10:21 de 31/01/2019, Dean Derbyshire escreveu:
>>> thanks all. I recon I have the ESRF data sorted.. but Daresbury.. am I 
>>> right in assuming MARCCD or are we going back as far as image plate?
>>> here is the image header
>>> Harry what do you think
>>> 
>>> HEADER_BYTES=  512;
>>> DIM=2;
>>> BYTE_ORDER=little_endian;
>>> TYPE=unsigned_short;
>>> PIXEL_SIZE=0.08160;
>>> BIN=none;
>>> ADC=slow;
>>> DETECTOR_SN=421;
>>> DATE=Wed Apr 13 17:59:22 2005;
>>> TIME=20.00;
>>> DISTANCE=125.000;
>>> OSC_RANGE=1.000;
>>> PHI=7.000;
>>> OSC_START=7.000;
>>> AXIS=phi;
>>> WAVELENGTH=1.48800;
>>> BEAM_CENTER_X=94.700;
>>> BEAM_CENTER_Y=96.400;
>>> UNIF_PED=1500;
>>> SIZE1=2304;
>>> SIZE2=2304;
>>> CCD_IMAGE_SATURATION=65535;
>>> }
>>> 
>>> 
>>> -Original Message-
>>> From: Dean Derbyshire
>>> Sent: den 31 januari 2019 10:50
>>> To: 'graeme.win...@diamond.ac.uk' ; 'Luca 
>>> Jovine' 
>>> Subject: RE: [ccp4bb] old data
>>> 
>>> ok may have lied.. not just 1 dataset i note.
>>> 
>>> Daresbury 14-1 on 19th April 2005. (I'm assuming MAR image plate but!)
>>> 
>>> ESRF ID23-1 on 4th September 2007.
>>> ESRF ID23-1 on 8th November 2007.
>>> ESRF ID23-1 on 25th June 2008.
>>> ESRF ID23-1 on 11th February2010.
>>> 
>>> I will post the headers in a sec
>>> 
>>> :)
>>> 
>>> -Original Message-
>>> From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk]
>>> Sent: den 31 januari 2019 10:42
>>> To: Dean Derbyshire 
>>> Cc: ccp4bb@jiscmail.ac.uk
>>> Subject: Re: [ccp4bb] old data
>>> 
>>> Hi Dean
>>> 
>>> Usually there is a serial number buried somewhere in the header - many 
>>> are text headers though some have TIFF format binary headers. Often a 
>>> timestamp as well though this is less common
>>> 
>>> From there biosync may help e.g.
>>> 
>>> http://biosync.sbkb.org/beamlineupdatehistory.jsp?region=european
>>> h_id=esrf_name=BM14=400=600
>>> 
>>> (the list of ESRF MX beamlines is short so should not be too painful)
>>> 
>>> Knowing the format, filename you can probably pin it down or if you 
>>> share a little more info someone on the BB will know
>>> 
>>> All the best Graeme
>>> 
>>> 
>>> 
>>> On 31 Jan 2019, at 09:38, Dean Derbyshire 
>>> mailto:dean.derbysh...@medivir.com>> wrote:
>>> 
>>> maybe a silly question it there a data base or other way to tell what 
>>> detector was used to collect historic data. Image header isn’t hugely 
>>> helpful ESRF is all I know for the source but I’d like to know what 
>>> the detector was at the time… -  I’m talking 2005-2010
>>> 
>>>  Dean Derbyshire
>>>  Principal Scientist Protein Crystallography [X]
>>>  Box 1086
>>>  SE-141 22 Huddinge
>>>  SWEDEN
>>>  Visit: Lunastigen 7
>>>  Direct: +46 8 54683219
>>>  Mobile: +46731251723
>>>  www.medivir.com
>>> --
>>>  This transmission is intended for the person to whom or the 
>>> entity to which it is addressed and may contain information that is 
>>> privileged, confidential and exempt from disclosure under applicable law.
>>> If you are not the intended recipient, please be notified that any 
>>> dissemination, distribution or copying is strictly prohibited.
>>> If you have received this transmission in error, please notify us 
>>> immediately.
>>> Thank you for your cooperation.
>>> 
>>> 

[ccp4bb] An overview of our crystallographic science

[Jrh Gmail]

Dear Colleagues,
I prepared this overview of our crystallographic science in Biosciences Reports 
at the invitation of the Biochemical Society, which I imagine you would be 
interested in:-
http://www.bioscirep.org/content/37/4/BSR20170204
It is open access.
All best wishes,
John 

Emeritus Professor John R Helliwell DSc

[ccp4bb] protein quantification with carbohydrates

[Gmail]

Dear all,

I have a (heavily and heterogeneously) glycosylated protein that has very low 
OD280 absorption. I wondered whether the glycans will have any effect on the 
accuracy of BCA or Bradford assay. Amino acid analysis doesn’t seem to be any 
better because carbohydrates will interfere with sample analysis and 
quantification. Any suggestion about other methods that we could try to measure 
the concentration of this protein? Much appreciated!

Best,
Tianyu

[ccp4bb] (Off-topic) Analogs of CDP-choline for crystallization

[Gmail]

Dear CCP4 members,

  I’m working on a phosphocholination pathway in which the enzyme utilizes the 
substrate Cytidine-diphosphate-choline (CDP-choline) as phosphocholione-donor.
  I’m enquiring about the possible analogs of CDP-choloine for 
cocrystallization with the enzyme as well as for the inhibition assays. 
  Many thanks to you in advance.

  Have a nice day!

  Wenhua Zhang

Re: [ccp4bb] Confusion about space group nomenclature

[Jrh Gmail]

Dear George
My student class would not find that IUCr dictionary definition helpful. What 
they do find helpful is to state that they cannot contain an inversion or a 
mirror. 
To honour Sohnke is one thing but is it really necessary as a label? You're 
from Huddersfield I am from Wakefield ie let's call a spade a spade (not a 
'Black and Decker'). 
Cheers
John

Prof John R Helliwell DSc

 On 2 May 2014, at 17:01, George Sheldrick gshe...@shelx.uni-ac.gwdg.de 
 wrote:
 
 In my program documentation I usually call these 65 the Sohnke space groups, 
 as defined by the IUCr: 
 http://reference.iucr.org/dictionary/Sohnke_groups  
 
 George
 
 
 On 05/02/2014 02:35 PM, Jim Pflugrath wrote:
 After all this discussion, I think that Bernhard can now lay the claim that 
 these 65 space groups should really just be labelled the Rupp space 
 groups.  At least it is one word. 
 
 Jim
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp 
 [hofkristall...@gmail.com]
 Sent: Friday, May 02, 2014 3:04 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Confusion about space group nomenclature
 ….
  
 Enough of this thread.
  
 Over and out, BR
 
 
 -- 
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry, 
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-33021 or -33068
 Fax. +49-551-39-22582
 

Re: [ccp4bb] Confusion about space group nomenclature

[Jrh Gmail]

Dear Gerard
I am duly reprimanded .
You are quite correct .
Have a good weekend
John

Prof John R Helliwell DSc

 On 2 May 2014, at 18:16, Gerard Bricogne g...@globalphasing.com wrote:
 
 Dear John,
 
 What is wrong with honouring Sohnke by using his name for something
 that he first saw a point in defining, and in investigating the properties
 resulting from that definition? Why insist that we should instead replace
 his name by an adjective or a circumlocution? What would we say if someone
 outside our field asked us not to talk about a Bragg reflection, or the
 Ewald sphere, or the Laue method, but to use instead some clever adjective
 or a noun-phrase as long as the name of a Welsh village to explain what
 these mean? 
 
 Again, I think we should have a bit more respect here. When there are
 simple adjectives to describe a mathematical properties, the mathematical
 vocabulary uses it (like a normal subgroup). However, when someone has
 seen that a definition by a conjunction of properties (i.e. something
 describable by a sentence) turns out to characterise objects that have much
 more interesting properties than just those by which they were defined, then
 they are often called by the name of the mathematician who first saw that
 there is more to them than what defines them. Examples: Coxeter groups, or
 Lie algebras, or the Leech lattice, or the Galois group of a field, the
 Cayley tree of a group ... . It is the name of the first witness to a
 mathematical phenomenon, just as we call chemical reactions by the name of
 the chemist who saw that mixing certain chemicals together led not just to a
 mixture of those chemicals.
 
 So why don't we give Sohnke what belongs to him, just as we expect
 other scientists to give to Laue, Bragg and Ewald what we think belongs to
 them? Maybe students would not be as refractory to the idea as might first
 be thought.
 
 
 With best wishes,
 
  Gerard.
 
 --
 On Fri, May 02, 2014 at 05:42:34PM +0100, Jrh Gmail wrote:
 Dear George
 My student class would not find that IUCr dictionary definition helpful. 
 What they do find helpful is to state that they cannot contain an inversion 
 or a mirror. 
 To honour Sohnke is one thing but is it really necessary as a label? You're 
 from Huddersfield I am from Wakefield ie let's call a spade a spade (not a 
 'Black and Decker'). 
 Cheers
 John
 
 Prof John R Helliwell DSc
 
 On 2 May 2014, at 17:01, George Sheldrick gshe...@shelx.uni-ac.gwdg.de 
 wrote:
 
 In my program documentation I usually call these 65 the Sohnke space 
 groups, as defined by the IUCr: 
 http://reference.iucr.org/dictionary/Sohnke_groups  
 
 George
 
 
 On 05/02/2014 02:35 PM, Jim Pflugrath wrote:
 After all this discussion, I think that Bernhard can now lay the claim 
 that these 65 space groups should really just be labelled the Rupp space 
 groups.  At least it is one word. 
 
 Jim
 
 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard 
 Rupp [hofkristall...@gmail.com]
 Sent: Friday, May 02, 2014 3:04 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] Confusion about space group nomenclature
 ….
 
 Enough of this thread.
 
 Over and out, BR
 
 
 -- 
 Prof. George M. Sheldrick FRS
 Dept. Structural Chemistry, 
 University of Goettingen,
 Tammannstr. 4,
 D37077 Goettingen, Germany
 Tel. +49-551-39-33021 or -33068
 Fax. +49-551-39-22582

Re: [ccp4bb] metals disapear

[Jrh Gmail]

Dear Dean
An example, albeit not a metal, can be found here:-
http://journals.iucr.org/s/issues/2007/01/00/xh5011/xh5011.pdf

Such specific damage has a long history:-
http://www.sciencedirect.com/science/article/pii/0022024888903223

An X-ray sensitive metals centre is the Mn5Ca OEC of PS II and details can 
found here :-
http://m.pnas.org/content/102/34/12047.long

But metals in proteins can also be robust to X-rays and eg verified by parallel 
non damaging neutron crystallographic studies such as on MnCa concanabalin A .

Best wishes
John

Prof John R Helliwell DSc

 On 30 Apr 2014, at 11:33, Dean Derbyshire dean.derbysh...@medivir.com wrote:
 
 Hi all,
 Has anyone experienced catalytic metal ions disappearing during data 
 collection ?
 If so, is there a way of preventing it?
 D.
  
Dean Derbyshire
Senior Research Scientist
 image001.jpg
Box 1086
SE-141 22 Huddinge
SWEDEN
Visit: Lunastigen 7
Direct: +46 8 54683219
www.medivir.com
  
 --
 This transmission is intended for the person to whom or the entity to which 
 it is addressed and may contain information that is privileged, confidential 
 and exempt from disclosure under applicable law. If you are not the intended 
 recipient, please be notified that any dissemination, distribution or copying 
 is strictly prohibited. If you have received this transmission in error, 
 please notify us immediately.
 Thank you for your cooperation.

[ccp4bb] IUCr Diffraction Data Deposition Working Group

[Jrh Gmail]

Dear Colleagues,
We wish to let you know that the Triennial report for 2011 to 2014 on 
diffraction data deposition matters, prepared by the IUCr Diffraction Data 
Deposition Working Group (DDD WG) is now available at:-
http://forums.iucr.org/viewtopic.php?f=21t=343
Best wishes,

John, Brian and Tom 

John Helliwell Chair of the WG;
Brian McMahon Co-Chair of the WG;
Tom Terwilliger Member representing the IUCr Commission on Biological 
Macromolecules

Re: [ccp4bb] twinning problem ?

[Jrh Gmail]

Dear Jacob
For a review of this topic see
http://www.tandfonline.com/doi/full/10.1080/08893110310001643551#.UyCVLikgGc0


I also refer you to the more recent OUP IUCr book Chayen, Helliwell and Snell 
ie which includes these topics:-
 
http://global.oup.com/academic/product/macromolecular-crystallization-and-crystal-perfection-9780199213252;jsessionid=5564F908743CCE57BAD506586B47B6CC?cc=gblang=en;

I declare a 'perceived conflict of interest' in making this book suggestion to 
you.

Best wishes
John

Prof John R Helliwell DSc

 On 12 Mar 2014, at 16:59, Keller, Jacob kell...@janelia.hhmi.org wrote:
 
 Not sure I understand why having statistical disorder makes for streaks--does 
 the crystal then have a whole range of unit cell constants, with the spot at 
 the most prevalent value, and the streaks are the tails of the 
 distribution? If so, doesn't having the streak imply a really wide range of 
 constants? And how would this be different from mosaicity? My guess is that 
 this is not the right picture, and this is indeed roughly what mosaicity is.
 
 Alternatively, perhaps the streaks are interpreted as the result of a duality 
 between the unit cell, which yields spots, and a super cell which is so 
 large that it yields extremely close spots which are indistinguishable from 
 lines/streaks. Usually this potential super cell is squelched by destructive 
 interference due to each component unit cell being very nearly identical, but 
 here the destructive interference doesn't happen because each component unit 
 cell differs quite a bit from its fellows.
 
 And I guess in the latter case the supercell would have its cell constant 
 (in the direction of the streaks) equal to (or a function of) the coherence 
 length of the incident radiation?
 
 I know some attempts have been (successfully) made to use diffuse scattering, 
 but has anyone used the streak intensities to determine interesting features 
 of the crystallized protein?
 
 JPK
 
 
 
 -Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew 
 Leslie
 Sent: Wednesday, March 12, 2014 12:25 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] twinning problem ?
 
 Dear Stephen,
 
   I have seen a similar effect in the structure of 
 F1-ATPase complexed with the full length inhibitor protein. The inhibitor is 
 a dimer, and it actually couples 2 copies of the ATPase, but it crystallised 
 with only one copy of the ATPase per asymmetric unit. When I solved the 
 structure by MR, I saw additional density that could not be accounted for. 
 The extra density was, in fact, a second ATPase molecule that was related to 
 the first by a 120 degree rotation about the pseudo 3-fold axis of the 
 enzyme. The dimers were packing with statistical disorder in the crystal 
 lattice. This gave rise to clear streaking between Bragg spots in the 
 diffraction images in a direction that was consistent with that expected from 
 the statistical packing of the inhibitor linked dimers.
 
 Two copies of F1 were included in the refinement, each with occupancy 0.5. 
 the final Rfree was 27.7% (2.8A data). Prior to introduction of the second 
 copy of F1, the Rfree was 37%.
 
 More details are in Cabezon et al., NSMB 10, 744-750, 2003
 
 Best wishes,
 
 Andrew
 
 
 
 On 11 Mar 2014, at 14:04, Stephen Cusack cus...@embl.fr wrote:
 
 Dear All,
  I have 2.6 A data and unambiguous molecular replacement solution 
 for two copies/asymmetric unit of a 80 K protein for a crystal integrated in 
 P212121 (R-merge around 9%) with a=101.8, b=132.2, c=138.9.
 Refinement allowed rebuilding/completion of the model in the noraml 
 way but the R-free does not go below 30%. The map in the model regions looks 
 generally fine but  there is a lot of extra positive density in the solvent 
 regions (some of it looking like weak density for helices and strands)  and 
 unexpected positive peaks within the model region.
 Careful inspection allowed manual positioning of a completely different, 
 overlapping solution for the dimer which fits the extra density perfectly.
 The two incompatible solutions are related by a 2-fold axis parallel to a.
 This clearly suggests some kind of twinning. However twinning analysis 
 programmes (e.g. Phenix-Xtriage), while suggesting the potentiality of 
 pseudo-merohedral twinning (-h, l, k) do not reveal any significant 
 twinning fraction and proclaim the data likely to be untwinned. (NB. 
 The programmes do however highlight a non-crystallographic translation and 
 there are systematic intensity differences in the data). Refinement, 
 including this twinning law made no difference since the estimated twinning 
 fraction was 0.02. Yet the extra density is clearly there and I know exactly 
 the real-space transformation between the two packing solutions.
 How can I best take into account this alternative solution (occupancy seems 
 to be around 20-30%) in the refinement ?
 thanks for your suggestions
 

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

[Gmail]

Dear colleagues, I am looking for structures of protein complexes in which 
N-linked glycans mediate inter-molecular protein-protein interactions. Can 
anyone point me in the right direction? Thanks!

Tianyu




Gmail via foxmail

[ccp4bb] Postdoctoral position in UC Irvine

[Gmail]

UNIVERSITY OF CALIFORNIA, IRVINE

DEPARTMENT OF PHYSIOLOGY  BIOPHYSICS

POSTDOCTORAL SCHOLAR

One postdoctoral position is available immediately in Dr. Rongsheng Jin’s 
laboratory at the Department of Physiology and Biophysics, UC Irvine, and will 
remain open until filled. The new postdoctoral scholar is expected to 
participate in one of two major research projects: the structural and 
functional characterization of ion channels, receptors, and signaling molecules 
at synapses, and the mechanism of action of bacterial virulence factors in 
their cellular context. Our laboratory employs a multidisciplinary approach 
that combines X-ray crystallography, SAXS, electron microscopy with the more 
traditional approaches of biochemistry and biophysics. We also have built 
long-standing collaborative relationships in the areas of cell biology, 
electrophysiology, toxicology, and animal studies. The successful candidates 
should have a Ph.D. degree, high motivation, and strong background in one or 
more of the following research areas: biochemistry, biophysics, molecular 
biology, and structural biology. Experience in insect cell and/or mammalian 
cell culture would be desirable, but is not required. Salary is commensurate 
with qualifications and experience. 

To apply for this position please send cover letter, curriculum vitae, and 
names of three references to Rongsheng Jin (r@uci.edu)

“The University of California, Irvine is an Equal Opportunity Employer 
committed to excellence through diversity.”

Re: [ccp4bb] need suggestions

[Flip GMAIL]

Hi Afshan,

Have look at http://www.douglas.co.uk/Scaling_Up.htm, Patrick has some 
general tips on scaling up. Elsewhere on his site you'll find tips for 
conversion to microbatch, you may want to try that out as well. I assume 
the screen crystals were not big enough to mount?


Flip

Op 4/16/2013 11:21, Afshan Begum schreef:


 Dear All,

I have encountered one problem to optimization the crystallization 
condition manually. Actually i got the good shape and even size 
crystal in a screening plate. The condition are :


20% PEG 6000, 0.1M MES pH 6.0 whereas protein in 10mM Na-acetate pH 
5.7 contain 50mM NaCl, 1mM EDTA 5mM BME.
When I tried to optimize this on Linbro the drops are become heavily 
precipitate even a mints. I tried so many things to avoid this ppt 
such as start PEG conc from 7%, dilute protein at half conc., add more 
salt in a reservoir solution but no succeeds.

The protein prep is same which was using to get the Hits.

I would be very thankful if you people give me nice suggestions.

Thanks

Best Regards

AFSHAN

Re: [ccp4bb] Bfactor is zero?

[Ezra's gmail]

On 12/20/2010 10:34 AM, Zhibing Lu wrote:

Hi All,
Recently I solved a structure in which some water molecules have 
Bfactors at 0  and overall wilson Bfactor is 0.654 based on PHENIX 
refinement. Is it possible?

Bill Lu

Hi Bill,

What resolution are you working with here?  An overall Wilson B 1 is 
sort of odd... If the resolution is too low - the
slope in the Wilson plot has a lot of play - and might be 
indetermiate  I would use phenix.xtriage and see if there are any 
indications of something interesting happening with your data...


Ezra

Re: [ccp4bb] .cv to .mtz conversion

[Ezra's gmail]

 On 9/28/2010 10:41 AM, Jeremiah Farelli wrote:

We recently had this problem in our lab.

No matter what we tried, we could not get convert2mtz (or any other program) to 
work properly.  We were probably doing something wrong with the fortran?

Depending on how far along you are, you can try using phenix.refine.  Just 
input your model and the .cv file and phenix will export a new .cv file with 
Free-R flags intact.

If you aren't to the model building stage yet, this won't work however.
Use the program sftools - sorry no GUI... It can handle CNS format - and 
will convert the test set flag conversion

from CNS (TEST=1) to CCP4 (=0)

Ezra

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

[Ezra's gmail]

 I cannot say what you have - running a gel, MS, etc of a washed crystal
could confirm what you have.
What you did not indicate is if your lack of diffraction was of frozen
or unfrozen crystals. I have seen too many cases where it is the cryo
condition killing diffraction. So if you have not tried yet - try a wet
mount.

Ezra

On 8/30/2010 9:24 PM, qiangm zhang wrote:
 Hi all,
 I got a crystal of one membrane protein (~60kD) from Na/K phosphate
 condition (see getit_4), then I got the improved crystal like getit_5
 after trying seeding, different detergents, lipids and additives. But
 this crystal does not diffract at all, I already tried Izit staining
 which shows it is protein crystal (detergent crystal?). Does anyone
 have any good suggestions for the optimization of this membrane
 protein crystallization? Thank you in advance.

 Best regards

 Qiangmin Zhang

 Biomedical Science Tower 3
 Room1034
 3501 Fifth Avenue
 Pittsburgh, PA 15260





 -- 
 张强敏

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

[Ezra's gmail]

 I cannot say what you have - running a gel, MS, etc of a washed crystal
could confirm what you have.
What you did not indicate is if your lack of diffraction was of frozen
or unfrozen crystals. I have seen too many cases where it is the cryo
condition killing diffraction. So if you have not tried yet - try a wet
mount.

Ezra

On 8/30/2010 9:24 PM, qiangm zhang wrote:
 Hi all,
 I got a crystal of one membrane protein (~60kD) from Na/K phosphate
 condition (see getit_4), then I got the improved crystal like getit_5
 after trying seeding, different detergents, lipids and additives. But
 this crystal does not diffract at all, I already tried Izit staining
 which shows it is protein crystal (detergent crystal?). Does anyone
 have any good suggestions for the optimization of this membrane
 protein crystallization? Thank you in advance.

 Best regards

 Qiangmin Zhang

 Biomedical Science Tower 3
 Room1034
 3501 Fifth Avenue
 Pittsburgh, PA 15260





 -- 
 张强敏

Re: [ccp4bb] Query regarding GST fusion protein purification

[Ezra's gmail]

 It sounds like list your GST construct is not binding to the column 
(or very well) when the peptidase is attached. GST needs to form a dimer 
to binding to the column - I suspect that your construct interferes with 
dimer formation - when the peptidase is present, but when not there due 
to stalled translation (rare codon?) it binds ok.   The other 
possibility is that when your peptidase is present it causes aggregation 
- preventing binding.  Maybe it depends on the concentration of your 
construct - possibly dilute and slow binding might work - but am not 
sure. Also - is there much of a linker between the GST and the peptidase?


Maybe others have a suggestion...

Good luck,

Ezra

On 8/29/2010 7:28 AM, Ashok Ranjan Nayak wrote:

Hello one and all !!

I have been working on cloning and purification aspects on a Leishmanial 
cysteine peptidase (pI= 8.2) for quite some time. I had cloned it in pGEX 
expression vector. Expression seemed quite okay when induced with 0.5 and 1mM 
IPTG, so did the solubility in 4 buffers at different pH conditions. i. e.  
Tris (6.8), HEPES (7.5), Bicine (pH = 9) and Glycine (pH=10). The problem is 
when I purify it using glutathione sepharose column I get only GST (size wise 
estimation; no western tried ) i.e. a  prominent 25 KD band. At the same time I 
get the fusion protein in the load, equilibration and  wash fractions. When I 
increased Nacl concentration upto 400 mM  I only could exclude the fusion 
protein band from wash. I had tried protease inhibitors like PMSF, sigma 
cocktail, and DTT in the lysate before sonication. I had also tried reduced 
glutathione upto 40 mM in the elution buffer with two different pH at 8 and 9.

 I also read from literature that similar intracellular cysteine 
proteases behave same even after mutating the conserved cysteine residue at its 
active site. They all say that its not because of autocatalytic property of the 
enzyme its because of some proteases from E.coli.

Should I try ion exchange or affinity chromatography using any inhibitor of 
this enzyme??

Can anyone suggest me some tip?? Guys help me out. i am  kind of struck here



Ashok Ranjan Nayak
Research Scholar
Molecular and Structural Biology Division
Central Drug Research Institute,
Lucknow