Re: [ccp4bb] Sub-angstrom resolution

[Dirk Kostrewa]

Dear Colin,

Am 10.01.12 18:08, schrieb Colin Nave:




3. The structure factors are lower for large unit cells. This will mean they 
will be harder to detect, particularly if there is a high background.



But aren't the total structure factors of a unit cell the sum of the 
atomic structure factors? For a larger unit cell (assuming a similar 
solvent content), I would then expect larger structure factors.


Best regards,

Dirk.

--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

[dusan turk]

Hi Guys,

I just want to make aware that apart form PRODRG etc there exist also PURY 
server http://pury.ijs.si/, which offers a possibility to create restraints for 
heteromolecules.   It accepts PDB files, smiles format. Alternatively JME 
editor can be used to draw your compound.

PURY: a database of geometric restraints of hetero compounds for refinement in 
complexes with macromolecular structures
Miha Andrejasˇicˇ, Jure Prazˇnikar and Dusˇan Turk
Acta Cryst. (2008). D64, 1093–1109)

Its parameters are extracted from CSD. Its unlimited use is restrained to the 
CSD license holders, whereas for a small number of downloads its use is not 
restrained.

dusan




Dr. Dusan Turk, Assoc. Prof.
Head of Structural Biology Group
Head of Centre for Protein  and Structure Production
Centre of excellence for Integrated Approaches in Chemistry and Biology of 
Proteins, Scientific Director
Professor of Structural Biology at IPS "Jozef Stefan"
e-mail: dusan.t...@ijs.sihttp://bio.ijs.si/sbl/
phone: +386 1 477 3857   Dept. of Biochem.& Mol.& Struct. Biol.
fax:   +386 1 477 3984   Jozef Stefan Institute
Jamova 39, 1 000 Ljubljana,Slovenia
Skype: dusan.turk (voice over internet: www.skype.com

[ccp4bb] Choice of heavy atom derivatives

[Federica Basilico]

Hi everyone,

I have crystals of a protein of 176 residues, with 5 Cys, 8 His, 3 Met.
Native crystals grow in 10% MPD, 100mM Bicine pH 9.0. They show a nice 
diffraction, but appear to be perfectly twinned.
I have crystallised a SeMet derivative, but I have not been able to 
collect sufficiently good data, to get the phases.

Thus, I was thinking of trying with some heavy atom soaks.
Given the characteristics of my protein and crystallisation conditions, 
which compounds and conditions would you advice as worth testing?
I am a beginner in crystallography, so all your suggestions would be 
precious to me...

Thanks in advance,

Federica

--
Federica Basilico
Ph.D. student
Department of Experimental Oncology
European Institute of Oncology
Via Adamello 16
20139 Milan (Italy)

Re: [ccp4bb] Sub-angstrom resolution

[Thomas Womack]

On 11 Jan 2012, at 02:13, Artem Evdokimov wrote:

> There are two sides to this qustion: the scientific one is actually easier to 
> answer in generic terms - but I also would like to point out the very recent 
> example of a mystery that required very high resoluton (and orthogonal 
> techniques) to answer, namely the puzzle of the light atom in the center of 
> the mofe nitrogenase protein. Highly recommended reading.
> 
That does sound interesting: could you give a reference?  I can find various 
papers about small slices of the puzzle, but not a review article.

Tom

Re: [ccp4bb] Choice of heavy atom derivatives

[Miguel Ortiz Lombardía]

Le 11/01/12 12:23, Federica Basilico a écrit :
> Hi everyone,
> 
> I have crystals of a protein of 176 residues, with 5 Cys, 8 His, 3 Met.
> Native crystals grow in 10% MPD, 100mM Bicine pH 9.0. They show a nice
> diffraction, but appear to be perfectly twinned.
> I have crystallised a SeMet derivative, but I have not been able to
> collect sufficiently good data, to get the phases.
> Thus, I was thinking of trying with some heavy atom soaks.
> Given the characteristics of my protein and crystallisation conditions,
> which compounds and conditions would you advice as worth testing?
> I am a beginner in crystallography, so all your suggestions would be
> precious to me...
> Thanks in advance,
> 
> Federica
> 
> --
> Federica Basilico
> Ph.D. student
> Department of Experimental Oncology
> European Institute of Oncology
> Via Adamello 16
> 20139 Milan (Italy)
> 

Hi,

This site may help:

http://hatodas.harima.riken.go.jp/

-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

[ccp4bb] DDM crystals

[Patrick Loll]

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 Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pat.l...@drexelmed.edu

Re: [ccp4bb] DDM crystals

[Jacob Keller]

What exactly is your question--I saw tons of "crystals" of DDM and
PEGs, I think especially P400, if I recall correctly.

JPK

On Wed, Jan 11, 2012 at 7:12 AM, Patrick Loll  wrote:
> 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 Graduate Program
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pat.l...@drexelmed.edu
>
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Another possibility - direct use of QM)

[Oliver Smart]

On Mon, 9 Jan 2012, krish wrote:



You can use Phenix.elbow or phenix.reel to load the coordinates of the 
small moleucle and optimize with AM1 (semi-empirical), then you should 
get reasonable geometirc parameters suc as bond length, bond angles and 
etc.  



Hope this helps !
 
Cheers,
Krishna
 
Krishna Chinthalapudi, PhD
Hannover Medical School


Shveta and Krishna,

Just to point out that an alternative to using QM methods as a source of 
ligand restraints for refinement is to directly use the methods to 
represent the ligand chemistry during refinement. BUSTER provides the 
facility to do this see:


http://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQMIntroduction

It is pretty easy to do, particularly for semi-empirical QM methods (such 
as AM1 or the superior RM1). An advantage is that instead of coming up 
with approximate restraints sourced from AM1 then the actual method itself 
is used.



Regards,

Oliver 
| Dr Oliver Smart |

| Global Phasing Ltd., Cambridge UK   |
| http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] Sub-angstrom resolution

[Thomas Womack]

On 11 Jan 2012, at 11:36, Thomas Womack wrote:

> 
> On 11 Jan 2012, at 02:13, Artem Evdokimov wrote:
> 
>> There are two sides to this qustion: the scientific one is actually easier 
>> to answer in generic terms - but I also would like to point out the very 
>> recent example of a mystery that required very high resoluton (and 
>> orthogonal techniques) to answer, namely the puzzle of the light atom in the 
>> center of the mofe nitrogenase protein. Highly recommended reading.
>> 
> That does sound interesting: could you give a reference?  I can find various 
> papers about small slices of the puzzle, but not a review article.

http://www.sciencemag.org/content/334/6058/974.full is the work using 
orthogonal techniques to figure out which the light atom actually was, with a 
discussion at
http://www.sciencemag.org/content/334/6058/914.full 

The high-resolution structure that revealed that there was a light atom there 
is from 2002: http://www.sciencemag.org/content/297/5587/1696.full with 
discussion at http://www.sciencemag.org/content/297/5587/1654.full

Tom

Re: [ccp4bb] Sub-angstrom resolution

[Colin Nave]

Dirk
Yes. Equating the square root of the measured intensity (photons/spot) to the 
structure factor was sloppy nomenclature on my part.

One should look at Darwin's formula for the intensity (photons/spot). The 
adverse term in it is Vxtal/Vcell (ratio between crystal and cell volumes).

Regarding the scaling behaviour of the structure factors with respect to Vcell, 
I think section 2.7 of the Holton and Frankel article gives good explanations 
(i.e. looking at the issue from more than one point of view). See 
The minimum crystal size needed for a complete diffraction data set, Acta 
Cryst. D, 66, 393-408 (2010).
http://journals.iucr.org/d/issues/2010/04/00/ba5148/ . 

In short, the scaling of the (squared) structure factors compensates for the 
other Vcell term in the Darwin formula leaving one with the remaining adverse 
Vxtal/Vcell. For the same size crystal doubling each cell edge leads to average 
spot intensities being reduced by a factor of 8.

Thanks!
  Colin




-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk 
Kostrewa
Sent: 11 January 2012 09:15
To: ccp4bb
Subject: Re: [ccp4bb] Sub-angstrom resolution

Dear Colin,

Am 10.01.12 18:08, schrieb Colin Nave:



> 3. The structure factors are lower for large unit cells. This will mean they 
> will be harder to detect, particularly if there is a high background.


But aren't the total structure factors of a unit cell the sum of the atomic 
structure factors? For a larger unit cell (assuming a similar solvent content), 
I would then expect larger structure factors.

Best regards,

Dirk.

-- 

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] Choice of heavy atom derivatives

[Francis E Reyes]

> They show a nice diffraction, but appear to be perfectly twinned.
In most cases, structures can be solved (and biological questions answered) in 
twinned cases. I wouldn't be discouraged. 

> I have crystallised a SeMet derivative, but I have not been able to collect 
> sufficiently good data, to get the phases.

What is 'good' data to you? What are you considering as 'bad' data? 

> I am a beginner in crystallography, so all your suggestions would be precious 
> to me... 


You've come to the right place. Seek advice from people who have solved 
structures within the last 5 years using modern software. You'd be surprised 
how good the software for structure solution/refinement is these days. 

> Thus, I was thinking of trying with some heavy atom soaks.

This by chance is not a  metalloprotein is it? No covalently bound heavy 
metals? (maybe you have done some biochemistry and found some heavy metal 
requirement for activity, purification, etc)

> which compounds and conditions would you advice as worth testing?

If your native crystals diffract well on a home source, I would try soaking a 
fresh 500 mM solution of KI (iodide) for 5-10 seconds and collect the anomalous 
signal at home. If it kills your crystals, move to more toxic things... 

> 
> Thanks in advance,
> 
> Federica
> 

Cheers,

F



-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

[ccp4bb] Gordon Research Conference on Diffraction Methods in Structural Biology

[Ana Gonzalez]

We are excited to invite you to the biannual Gordon Conference on
Diffraction Methods in Structural Biology, which will be held at Bates
College in Lewiston, Maine from July 15-20.

Behind all the new biological systems that are being studied by
diffraction methods nowadays lie a compendium of methods, from
crystallization to structure solution and refinement.  Moreover, the
use of complementary techniques to fully understand structural systems
is gaining importance, and the 4th generation x ray sources ("x-ray
lasers") are promising breakthrough capabilities.

We have put together a program covering all these methodological
aspects, but also highlighting some of the most exciting new
structural biology that has taken place over the last couple of years.
As usual, we left open a whole session exclusively for presentations
that will be selected from the late-afternoon posters sessions, which
take place in the first few days of the meeting: you will have a
chance to impress the selection jury with your poster presentation, and
get the opportunity to present your work on the last day of the
meeting.

Most of the leading methods developers and quite a few prominent 
structural biologists will be present for the duration of the meeting, 
which has a relaxed format with free afternoons, providing ample 
opportunities for informal discussions, outdoors activities, and 
showcasing your skills in football/soccer.


The preliminary program and details on the application procedure are 
available at:

http://www.grc.org/programs.aspx?year=2012&program=diffrac

The Gordon Research Conference offers fellowships for underrepresented
minority members attending a conference for the first time. See:
http://www.grc.org/diversity.aspx

Very limited  funding on a first come first served basis is also available
for international minority graduate students or post docs, scientists
working in Eastern European or Former Soviet Union countries and research
active scientists from "Predominantly Undergraduate Institutions" (NSF
definition ). Eligible applicants should contact directly the conference
chair.

We hope to see you there !

Ana Gonzalez (Chair) & Tassos Perrakis (Vice-Chair)
--
---
   Ana Gonzalez 
  Staff Scientist
 Stanford Synchrotron Radiation Lightsource
2575 Sand Hill Road, MS 99
   Menlo Park  CA 94025
 Phone: (650) 926 8682 Fax: (650) 926 3292
---

[ccp4bb] brainpool research associate position

[intekhab alam]

Dear members
Have a look on the advertisement for the position of research associate in
structural biology.
Interested candidates please reply to kh...@korea.ac.kr. Informal enquiries
can also be made.



Structural Bioinformatics Lab, Department of Biotechnology &
Bioinformatics, Korea University, Seoul Korea

Brainpool Research Associate – Full time, fixed term appointment for up to
two years



The Structural Bioinformatics Lab is seeking a Brainpool Research Associate
to carry out structural analysis (x-ray crystallography) and biophysical
studies of complexes related to virus-host interaction. The group is led by
Professor Kyung Hyun Kim and has over the years produced good results
(PNAS, NAR, JGV). The research programme is funded by a grant from the
Korean Federation of Science and technology Societies
(www.brainpool.or.kr)
to which both the applicant and our team apply together. Further details on
the research group can be found at http://sbl.korea.ac.kr/.



Applicants should have a PhD in Structural Biology, Biophysics or a related
area, with at least 5 years of research experience after Ph.D., or high
profile publications in the highest impact journals.



Salary range will be from $45,000-$55,000 per annum plus plane ticket,
moving expense and medical insurance. Initial salary for possibly the two
months will be dependent on the skills and experience of the successful
applicant.



Closing date for completed applications: 5 February 2012. To apply for this
position please send emails to kh...@korea.ac.kr with your resume.



Korea U is an equal opportunities employer and encourages applications from
all candidates irrespective of gender, race, disability, sexual
orientation, age, religion and belief or another protected characteristic.

-- 
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL

[ccp4bb] a question on Average Occupancy-weighted avg temperature factor (Deviation)

[Dialing Pretty]

Dear All,
 
For the RCSB depositation report, it gives the "Average Occupancy-weighted avg 
temperature factor (Deviation)".
 
Will you please tell me what range the "Average Occupancy-weighted avg 
temperature factor (Deviation)" should be and what is the significance of that 
value?
 
I am looking forward to getting your reply.
 
Cheers,
 
Dialing

[ccp4bb] Lithium versus Sodium

[Scott Pegan]

Hey all,

Does anyone know of a good article that deals with differentiating between
a lithium ion and sodium ion for density in a X-ray structures?

Scott

-- 
Scott D. Pegan, Ph.D.
Assistant Professor
Chemistry & Biochemistry
University of Denver
Office: 303 871 2533
Fax: 303 871 2254