Re: [ccp4bb] suggestion on protein crystallization optimization from phase separation

[Phoebe A. Rice]

We had a complex many years ago that could sometimes be convinced to 
crystallize by poking the drops (probably with a hair): if I remember 
correctly, both poking some of the skin into the drop and pulling some of the 
oily goo into more contact with the aqueous phase.  Then again, that complex 
also sometimes crystallized without help, so it might not be the best example 
for your case.

My group has generally found that the most important variable is the ends of 
the DNA, and often when we get the "winner" DNA we get at least crappy 
microcrystals under a variety of conditions.

Hope you get nice fat crystals soon!
 Phoebe


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Johannes Cramer 
[johannes.cra...@gmail.com]
Sent: Friday, April 07, 2017 7:37 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] suggestion on protein crystallization optimization from 
phase separation

Dear Joseph,

You have probably already done so, but have you tried in- or decreasing your 
protein+DNA concentration?
I had a similar problem with proteins that were concentrated too low. I had to 
increase protein and decrease Ammonium sulfate (precipitant in my case) 
concentration.

Cheers,
Johannes


2017-04-06 17:16 GMT+02:00 Joseph Ho 
>:
Dear all:

I would like to seek your suggestion on protein crystallization from
phase separation.
We recently observed many small round droplets shown in our
protein/DNA crystallization. Condition are 0.8M-1.6M LiSO4; 20mM
MgCl2; pH 5-8;  protein conc. ~15mg/ml). The UV microscope confirms
those are protein-rich phase separation.
We have tried to change conc. of LiSO4 and pH. Still we got different
size and amount of small round droplets. At 20 degree, those droplets
appear within one day and at 4 degree, it takes two-three days.  We
also tried additive and silver bullet screen. So far, we have not
found a condition to have protein crystals. The protein is already
truncated. Several DNA constructs are on-going.
At this point, I would like to seek your advice on the method to
optimize the condition. Based on


PS. Any people have luck with protein crystallization by streaking the
Gelationous protein to new drop as shown in
http://xray.bmc.uu.se/terese/tutorial3.html . Can you please share
your experience with us?

Thanks for your help.

Joseph Ho

[ccp4bb] Voltage-Gated Structures

[Keller, Jacob]

Dear Crystallographers,

Is anyone aware of examples of membrane proteins for which voltage-activated 
and -inactivated structures are both known? Homologs would work too, but I 
found it difficult to sift through the PDB for this, even searching for 
"voltage-gated." Any help would be appreciated-I would like to see an example 
of what the voltage gating conformational change is like.

All the best,

Jacob Keller

***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***

[ccp4bb] Crystallography summer school, St Andrews

[Tracey Gloster]

The University of St Andrews will be hosting a protein crystallography summer 
school once again this year, which will take place 20-26 August.

The course aims to cover the theoretical and practical aspects of protein 
crystallography from protein expression and purification, through crystal 
growth to data collection on in-house and synchrotron sources, phasing methods, 
automated model building and phase extension, refinement, and validation. 
Hands-on sessions in data processing (XIA2, DIALS), molecular replacement, 
MAD/SAD phasing, refinement and electron density map interpretation (in COOT) 
will be included.

The School is intended for first/second year postgraduates or postdocs new to 
crystallography. The week is very intensive, and gives a concentrated overview 
of the methods which many find useful.

As in the past, priority is given to UK applicants because of the funding 
arrangements, but is open to a limited number of overseas applicants.

For further details and the application form please see 
https://synergy.st-andrews.ac.uk/bsrc/

Tracey Gloster (University of St Andrews)
Johan Turkenburg (University of York)

Re: [ccp4bb] CCP4BB Digest - 5 Apr 2017 to 6 Apr 2017 (#2017-95)

[Massimo Domenico Sammito]

Dear all,
Regarding the job submission in SLURM from CCP4i, I wanted to add that it is 
possible for ARCIMBOLDO jobs to do it directly from the interface, you need to 
specify the path to a configuration file containing the required informations. 
More info on this configuration file are found here:
http://chango.ibmb.csic.es/installation
If you need any help for the configuration you can write back to me anytime. 

Best wishes,

Massimo Sammito

> Il giorno 07 apr 2017, alle ore 01:01, CCP4BB automatic digest system 
>  ha scritto:
> 
> There are 7 messages totaling 992 lines in this issue.
> 
> Topics of the day:
> 
>  1. ccp4/coot on macOSSierra (3)
>  2. How to submit to SLURM from CCP4i
>  3. suggestion on protein crystallization optimization from phase separation
>  4. Post-doc in membrane protein structural biology, Pfizer Inc
>  5. Reminder: Structural biologist in metabolic diseases, SGC University of
> Oxford
> 
> --
> 
> Date:Thu, 6 Apr 2017 08:59:24 +
> From:"POHL, EHMKE" 
> Subject: ccp4/coot on macOSSierra
> 
> Dear ccp4 community,
> 
>   I would appreciate any suggestions how to get the ccp4 interfaces (ccp4 and 
> ccp4i2) and coot running on the new MacBook Pro under macOS Sierra 10.12.3. 
> control. I have already tried different Xquartz version with no success
> 
> thanks so much
> 
> Ehmke
> 
> --
> 
> Date:Thu, 6 Apr 2017 10:52:47 +0100
> From:Nikos Pinotsis 
> Subject: Re: ccp4/coot on macOSSierra
> 
> Hi Ehmke,
> 
> for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This 
> set up works for me (including pymol etc)
> 
> good luck
> 
> Nikos
> 
> Dr. Nikos Pinotsis
> Institute of Structural and Molecular Biology
> Department of Biological Sciences, 3rd Floor, R313
> Birkbeck College
> Malet Street
> London WC1E 7HX
> T: +44 (0)207 631 6827
> F: +44 (0)207 631 6803
> M: +44 (0)792 384 3593
> 
>> On 06/04/2017 09:59, POHL, EHMKE wrote:
>> Dear ccp4 community,
>> 
>>   I would appreciate any suggestions how to get the ccp4 interfaces 
>> (ccp4 and ccp4i2) and coot running on the new MacBook Pro under macOS 
>> Sierra 10.12.3. control. I have already tried different Xquartz 
>> version with no success
>> 
>> thanks so much
>> 
>> Ehmke
> 
> --
> 
> Date:Thu, 6 Apr 2017 11:56:57 +0200
> From:Didier Spittler 
> Subject: Re: ccp4/coot on macOSSierra
> 
> Hello Nikos,
> 
> I use Zquartz 2.7.9 too and it works fine for me.
> 
> Best,
> 
> Didier
> 
> 2017-04-06 11:52 GMT+02:00 Nikos Pinotsis :
> 
>> Hi Ehmke,
>> 
>> for sierra 10.12.3 try with the Xquartz 2.7.9 (xorg-server 1.17.4). This
>> set up works for me (including pymol etc)
>> 
>> good luck
>> 
>> Nikos
>> 
>> Dr. Nikos Pinotsis
>> Institute of Structural and Molecular Biology
>> Department of Biological Sciences, 3rd Floor, R313
>> Birkbeck College
>> Malet Street
>> London WC1E 7HX
>> T: +44 (0)207 631 6827 <+44%2020%207631%206827>
>> F: +44 (0)207 631 6803 <+44%2020%207631%206803>
>> M: +44 (0)792 384 3593 <+44%207923%20843593>
>> 
>> On 06/04/2017 09:59, POHL, EHMKE wrote:
>> 
>> Dear ccp4 community,
>> 
>>   I would appreciate any suggestions how to get the ccp4 interfaces (ccp4
>> and ccp4i2) and coot running on the new MacBook Pro under macOS Sierra
>> 10.12.3. control. I have already tried different Xquartz version with no
>> success
>> 
>> thanks so much
>> 
>> Ehmke
>> 
>> 
>> 
> 
> 
> -- 
> Didier Spittler, PhD
> Phone number : +33658576481
> 
> --
> 
> Date:Thu, 6 Apr 2017 14:31:35 +0200
> From:Jesper Lykkegaard Karlsen 
> Subject: How to submit to SLURM from CCP4i
> 
> #!/bin/bash
> #
> # Simple script for submitting ccp4i jobs to the SLURM queuing system
> # Hack inspired from the ccp4i_condorsub script by Ronan Keegan
> #
> # Jesper Lykkegaard Karlsen 06/04/2017
> #
> 
> # Takes the ccp4i job com file as input
> infile=$2
> 
> # Get the def file location, name and the job number
> def_file_line=`grep \.def $infile`
> def_file=${def_file_line##*-r}
> def_file_name=${def_file##*/}
> job_number_name=${def_file_name%.*}
> 
> # Define and make scratch dir on remote FS
> CCP4_REM_SCR=$HOME/.ccp4_rem_scr
> if [ ! -d $CCP4_REM_SCR ]; then
>mkdir $CCP4_REM_SCR
> fi
> 
> # Move def_file to CCP4_REM_SRC and define new var
> cp -a $def_file $CCP4_REM_SCR/
> 
> # Get the project name from the def file
> project_line=`grep CCP4I $def_file | grep PROJECT `
> project=${project_line##* }
> 
> # Create the condor submission script
> cat << eof > ${CCP4_REM_SCR}/${job_number_name}_${project}_sbatch.sub
> #!/bin/bash
> #SBATCH -N1
> #SBATCH --share
> #SBATCH -o ${CCP4_REM_SCR}/${job_number_name}_${project}_sbatch.out
> 
> source /etc/profile.d/modules.sh
> module load 

Re: [ccp4bb] suggestion on protein crystallization optimization from phase separation

[Johannes Cramer]

Dear Joseph,

You have probably already done so, but have you tried in- or decreasing your
protein+DNA concentration?
I had a similar problem with proteins that were concentrated too low. I had
to increase protein and decrease Ammonium sulfate (precipitant in my case)
concentration.

Cheers,
Johannes


2017-04-06 17:16 GMT+02:00 Joseph Ho :

> Dear all:
>
> I would like to seek your suggestion on protein crystallization from
> phase separation.
> We recently observed many small round droplets shown in our
> protein/DNA crystallization. Condition are 0.8M-1.6M LiSO4; 20mM
> MgCl2; pH 5-8;  protein conc. ~15mg/ml). The UV microscope confirms
> those are protein-rich phase separation.
> We have tried to change conc. of LiSO4 and pH. Still we got different
> size and amount of small round droplets. At 20 degree, those droplets
> appear within one day and at 4 degree, it takes two-three days.  We
> also tried additive and silver bullet screen. So far, we have not
> found a condition to have protein crystals. The protein is already
> truncated. Several DNA constructs are on-going.
> At this point, I would like to seek your advice on the method to
> optimize the condition. Based on
>
>
> PS. Any people have luck with protein crystallization by streaking the
> Gelationous protein to new drop as shown in
> http://xray.bmc.uu.se/terese/tutorial3.html . Can you please share
> your experience with us?
>
> Thanks for your help.
>
> Joseph Ho
>

[ccp4bb] Join the editorial team of IUCr Journals

[Louise Jones]

Dear All

We are now seeking a number of new Editors and Co-editors for IUCr 
Journals, including our biological journals




Acta Crystallographica Section D, Structural Biology
and
Acta Crystallographica Section F, Structural Biology Communications

Full details are available at
http://www.iucr.org/news/notices/announcements/chesternotice_2017_04

Best wishes
Louise
_

Louise Jones
Managing Editor
Acta Cryst. D and Acta Cryst. F
International Union of Crystallography