[ccp4bb] Postdoc in Structure-Based Ligand Discovery, Shoichet Lab UCSF

2021-07-01 Thread Brian Shoichet 
*Postdoc in Structure-Based Ligand Discovery*

We are recruiting for a post-doctoral position in structure-based ligand
discovery in the Shoichet lab at the University of California San Francisco
(UCSF) (https://bkslab.org/) (https://bkslab.org/people/current_members). We
are particularly interested in recruiting investigators with protein
biochemistry and crystallography backgrounds interested in training in
structure-based drug discovery.


Research focuses on developing and testing new ligand discovery methods,
with a GPCR focus.  Open projects include structure-based discovery of new
analgesics, GPCR deorphanization, antiviral discovery against SARS-2, and
particularly biophysical testing of new docking methods in experimental
model systems. Recent papers include:


Tummino et al., *Science *2021


Schuller et al., *Science Adv* 2021


Pottel et al., *Science* 2020


Stein et al., *Nature *2020


Lyu et al., *Nature* 2019




Top facilities are available in a friendly, collaborative environment, and
the lab is well-resourced.  Stipend and benefits at or above NRSA levels.
If interested please send a cover letter, CV and contact information for
three referees to Brian Shoichet (shoic...@cgl.ucsf.edu).   Deadline Aug
15, 2021.


-- 
Brian Shoichet, Professor, UCSF
latest science from the lab:  *http://www.bkslab.org/
*



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[ccp4bb] Postdoctoral position in Structural Biology and Function of Neurotransmitter Transport (San Francisco)

2021-07-01 Thread Robert Stroud 
STRUCTURAL BIOLOGY AND FUNCTION OF NEUROTRANSMITTER TRANSPORT

 A post-doctoral position is available in the laboratory of Dr. Robert M. 
Stroud at the mission bay campus of the University of California San Francisco 
(UCSF). (https://msg.ucsf.edu/people/robert-stroud-ma-phd 
). Research in our group is 
focused on the structure and mechanisms of transmembrane processes, and 
particularly in this position on the mechanisms and regulation of transporters 
that package neurotransmitters into synaptic vesicles in the nervous system and 
the brain. These provide for the ‘quantal release’ in neuronal signaling. 
Structures are determined by cryo-electron microscopy, cryo-electron 
tomography, X-ray diffraction as inroads to defining the structural basis of 
function. This also involves expression and purification of membrane proteins, 
or complexes, use of detergents, and nanodiscs, and assays of transport in 
vesicles and in cells. Example see 
(https://www.ncbi.nlm.nih.gov/pubmed/32439795 
). Experience in cryo-EM and any 
of these areas is an advantage. First rate facilities are available in a highly 
collaborative environment. NRSA postdoctoral stipend levels+benefits. If 
interested please send a brief cover letter, CV and contact information for 
three persons who might provide references to Robert Stroud 
(str...@msg.ucsf.edu )  Deadline July31st

Robert Stroud
str...@msg.ucsf.edu






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Re: [ccp4bb] Co crystalization with less soluble ligand.

2021-07-01 Thread Steven Herron 

Fatty acids are very soluble in glycerol or the PEGs.

Most proteins tolerate high concentrations (30-50%) glycerol and PEGs.� 
So, it is quite possible to make a solution that will allow the protein 
crsytal and the ligand to both be in the same solution.


One of my former colleagues was in charge of dosing mice for drug 
testing.� He often had to get hydrophobic compounds into solution long 
enough to feed the compounds to the mice.


If the key compound is not soluble in the current system, change the 
system.


Some might complain that this is a lot of work (which it might be), but 
that might also be why no one else has done it yet.




On 6/23/2021 5:53 AM, Tim Gruene wrote:

Hi Frank,

heme becomes near completely insoluble when it dimerizes. Fatty acids
are also very insoluble. It is quite hard to get them into HSA, as far
as I remember.

Cheers,
Tim

On Wed, 23 Jun 2021 10:33:42 +0100 Frank von
Delft  wrote:


And then of course, you need to decide whether you at all care to
know anything about a compound that is so insoluble that it needs
that kind of treatment  :)

On 23/06/2021 09:52, hoh wrote:

Hi

As total insolubility does not exist, I regularly use another
method, which is to deposit a grain of the ligand directly into the
drop.

In this case, we no longer control the concentration. The goal is
to regularly freeze crystals (1 hour, 2 days, 1 week ..). Depending
on the results, it is possible to adjust the time. If after one
hour, the crystal no longer diffracts, redo the experience by
freezing at 10s, 30s, 2mn ..). If a blob appears, frozen after 1
week. This technique needs 2 things
, time and several exploitable crystals in the drop.


FH
  



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Re: [ccp4bb] Rmeas in DIALS?

2021-07-01 Thread Huw Jenkins 
Hi Graeme,

> On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) 
>  wrote:
> 
> Total observations   1432839600 559
> Total unique  418512397 494
> Assuming spacegroup: P 41 21 2
> Other likely alternatives are:
> P 43 21 2
> Unit cell:
>  78.580  78.580  36.950
>  90.000  90.000  90.000

Those cell params and no. reflections exactly match the ones from XDS shown in 
the i2 report. Are the DIALS ones from xia2 different to those shown in the 
report?

Thanks,


Huw


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Re: [ccp4bb] Rmeas in DIALS?

2021-07-01 Thread Winter, Graeme (DLSLtd,RAL,LSCI) 
Hi Phil,

No argument, you _can_

The question is where it came from in this context, as the outer shell is 
positive in the text output but somehow -ve in i2 version of the same

Unless i2 recalculates merging stats?

All the best Graeme

On 1 Jul 2021, at 14:52, Phil Evans 
mailto:p...@mrc-lmb.cam.ac.uk>> wrote:

You can get a negative Rmeas in a shell where  is negative

Sent from my iPhone

On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:

 Thanks for sending the logs

Looking at the output the negative R values don’t come from xia2 directly

For AUTOMATIC/DEFAULT/NATIVE OverallLow High
High resolution limit   1.012.741.01
Low resolution limit   36.95   36.971.03
Completeness   68.672.216.3
Multiplicity3.4 4.0 1.1
I/sigma 6.811.0 0.6
Rmerge(I) 0.127   0.131   1.543
Rmerge(I+/-)  0.121   0.127   1.173
Rmeas(I)  0.141   0.147   2.162
Rmeas(I+/-)   0.145   0.151   1.659
Rpim(I)   0.059   0.062   1.512
Rpim(I+/-)0.078   0.079   1.173
CC half   0.985   0.971   0.149
Wilson B factor  11.910
Anomalous completeness 45.757.6 1.8
Anomalous multiplicity  2.1 2.5 1.0
Anomalous correlation-0.106  -0.135   0.000
Anomalous slope   0.921
dF/F  0.079
dI/s(dI)  0.699
Total observations   1432839600 559
Total unique  418512397 494
Assuming spacegroup: P 41 21 2
Other likely alternatives are:
P 43 21 2
Unit cell:
 78.580  78.580  36.950
 90.000  90.000  90.000

While a 1990’s reviewer would have a hard time with those merging stats, I have 
seen worse and they seem internally consistent

I wonder, is ccp4i2 doing something itself which arrives at those numbers?

i2 devs - thoughts?

Thanks Graeme

On 1 Jul 2021, at 05:49, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:

Something odd happening there - please could you send the text log off list? 
i.e. xia2.txt

Thanks Graeme

On 1 Jul 2021, at 00:58, Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:

Why Rmeas is negative in DIALS output?


Thanks




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Re: [ccp4bb] Rmeas in DIALS?

2021-07-01 Thread Phil Evans 
You can get a negative Rmeas in a shell where  is negative 

Sent from my iPhone

> On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) 
>  wrote:
> 
>  Thanks for sending the logs
> 
> Looking at the output the negative R values don’t come from xia2 directly
> 
> For AUTOMATIC/DEFAULT/NATIVE OverallLow High
> High resolution limit   1.012.741.01
> Low resolution limit   36.95   36.971.03
> Completeness   68.672.216.3
> Multiplicity3.4 4.0 1.1
> I/sigma 6.811.0 0.6
> Rmerge(I) 0.127   0.131   1.543
> Rmerge(I+/-)  0.121   0.127   1.173
> Rmeas(I)  0.141   0.147   2.162
> Rmeas(I+/-)   0.145   0.151   1.659
> Rpim(I)   0.059   0.062   1.512
> Rpim(I+/-)0.078   0.079   1.173
> CC half   0.985   0.971   0.149
> Wilson B factor  11.910
> Anomalous completeness 45.757.6 1.8
> Anomalous multiplicity  2.1 2.5 1.0
> Anomalous correlation-0.106  -0.135   0.000
> Anomalous slope   0.921
> dF/F  0.079
> dI/s(dI)  0.699
> Total observations   1432839600 559
> Total unique  418512397 494
> Assuming spacegroup: P 41 21 2
> Other likely alternatives are:
> P 43 21 2
> Unit cell:
>  78.580  78.580  36.950
>  90.000  90.000  90.000
> 
> While a 1990’s reviewer would have a hard time with those merging stats, I 
> have seen worse and they seem internally consistent
> 
> I wonder, is ccp4i2 doing something itself which arrives at those numbers?
> 
> i2 devs - thoughts?
> 
> Thanks Graeme
> 
>>> On 1 Jul 2021, at 05:49, Winter, Graeme (DLSLtd,RAL,LSCI) 
>>>  wrote:
>>> 
>>> Something odd happening there - please could you send the text log off 
>>> list? i.e. xia2.txt
>>> 
>>> Thanks Graeme
>>> 
>>> On 1 Jul 2021, at 00:58, Murpholino Peligro  wrote:
>>> 
>>> Why Rmeas is negative in DIALS output?
>>> 
>>> 
>>> Thanks
>>> 
>>> 
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>> 
>>> 
>> 
>>  
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Re: [ccp4bb] Rmeas in DIALS?

2021-07-01 Thread Winter, Graeme (DLSLtd,RAL,LSCI) 
Thanks for sending the logs

Looking at the output the negative R values don’t come from xia2 directly

For AUTOMATIC/DEFAULT/NATIVE OverallLow High
High resolution limit   1.012.741.01
Low resolution limit   36.95   36.971.03
Completeness   68.672.216.3
Multiplicity3.4 4.0 1.1
I/sigma 6.811.0 0.6
Rmerge(I) 0.127   0.131   1.543
Rmerge(I+/-)  0.121   0.127   1.173
Rmeas(I)  0.141   0.147   2.162
Rmeas(I+/-)   0.145   0.151   1.659
Rpim(I)   0.059   0.062   1.512
Rpim(I+/-)0.078   0.079   1.173
CC half   0.985   0.971   0.149
Wilson B factor  11.910
Anomalous completeness 45.757.6 1.8
Anomalous multiplicity  2.1 2.5 1.0
Anomalous correlation-0.106  -0.135   0.000
Anomalous slope   0.921
dF/F  0.079
dI/s(dI)  0.699
Total observations   1432839600 559
Total unique  418512397 494
Assuming spacegroup: P 41 21 2
Other likely alternatives are:
P 43 21 2
Unit cell:
 78.580  78.580  36.950
 90.000  90.000  90.000

While a 1990’s reviewer would have a hard time with those merging stats, I have 
seen worse and they seem internally consistent

I wonder, is ccp4i2 doing something itself which arrives at those numbers?

i2 devs - thoughts?

Thanks Graeme

On 1 Jul 2021, at 05:49, Winter, Graeme (DLSLtd,RAL,LSCI) 
mailto:graeme.win...@diamond.ac.uk>> wrote:

Something odd happening there - please could you send the text log off list? 
i.e. xia2.txt

Thanks Graeme

On 1 Jul 2021, at 00:58, Murpholino Peligro 
mailto:murpholi...@gmail.com>> wrote:

Why Rmeas is negative in DIALS output?


Thanks




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Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom




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Re: [ccp4bb] How to process two datasets 45 degrees apart?

2021-07-01 Thread Andrew Leslie - MRC LMB 
Dear Murpholino,

Assuming that the two datasets are from the same 
crystal, and collected without moving the crystal in-between, then when 
processing with mosflm I recommend processing both sweeps in the same mosflm 
run. This is because you will get more accurate cell parameters using data from 
both sweeps, due to the wider phi range.

Best wishes,

Andrew



> On 1 Jul 2021, at 00:57, Murpholino Peligro  wrote:
> 
> Hi...
> I have a couple of datasets:
> A: From 0 to 45
> B: From 90 to 135
> 
> Can I process them as a unique data set? (with XDS or maybe Mosflm) or should 
> I process them apart and then merge them? 
> 
> 
> Thanks
> 
> 
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> 



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Re: [ccp4bb] How to process two datasets 45 degrees apart?

2021-07-01 Thread Tim Gruene 
Dear Murpholino,

in addition to Graeme's explanation w.r.t. XDS, you probably want to
also set the 'STARTING_ANGLE= 90', when you copy  
UNIT_CELL_A-AXIS=
UNIT_CELL_B-AXIS= 
UNIT_CELL_C-AXIS= 
from XDS_ASCII.HKL of the first data set into XDS.INP of the second
one.

Depending on the spacegroup and cell axes, just REFERENCE_DATA_SET=
together with SPACE_GROUP_NUMBER= and UNIT_CELL_CONSTANTS= might be
sufficient.

As a thrid option, you can treat it as one data set and make use of 
EXCLUDE_DATA_RANGE= 46 89 and integrate the data as a single data set.
The latter is probably the most fool proof approach, as long as the
file names for B are numbered 90 to 135.

Best wishes,
Tim


for the second data set
On Wed, 30 Jun 2021 18:57:03 -0500 Murpholino Peligro
 wrote:

> Hi...
> I have a couple of datasets:
> A: From 0 to 45
> B: From 90 to 135
> 
> Can I process them as a unique data set? (with XDS or maybe Mosflm) or
> should I process them apart and then merge them?
> 
> 
> Thanks
> 
> 
> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgpChgp68KG90.pgp
Description: OpenPGP digital signature

[ccp4bb] PhD position (Denmark), Structural biology with a focus on metabolite uptake

2021-07-01 Thread Bjørn Panyella Pedersen 
Dear colleagues,
Please pass this open PhD position along to anyone who might be interested. 
Thanks!
jobRxiv link: https://bit.ly/3Ak5Far

All the best,
/Bjørn


STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in 
metabolite transport

A PhD position is available in membrane protein biochemistry and structural 
biology in the research group of Dr. Bjørn P Pedersen at the Department of 
Molecular Biology and Genetics, Aarhus University, Denmark. The group studies 
the structure-function relationship of membrane proteins involved in metabolite 
uptake, primarily sterol and sugar uptake, as well as their regulation from a 
structural perspective (see http://pedersenlab.dk).

The PhD project will be developed in discussion with the selected candidate, 
but will involve expression, purification and structural/functional 
characterization of membrane proteins involved in metabolite uptake. Example 
see https://pubmed.ncbi.nlm.nih.gov/31543266/.

Structures are determined by cryo-electron microscopy, cryo-electron tomography 
and X-ray diffraction. This also involves expression and purification of 
membrane proteins, or complexes, use of detergents, and nanodiscs, and assays 
of transport in vesicles and in cells. First rate facilities are available in a 
highly cooperative environment.

The project is fully funded by the European Research Council (ERC). It would 
ideally suit an outstanding biochemistry graduate with a strong interest in 
structural biology. The candidate should have molecular biology, protein 
production and purification experience. Experience with membrane proteins or 
protein structure determination will be an advantage. Full training will be 
provided in all necessary areas of protein biochemistry and structural biology. 
Good English language skills are essential. Salary will be according to the 
collective agreement between the Danish Confederation of Professional 
Associations and the Danish State. The position will be filled as soon as a 
suitable candidate is identified, but start date is negotiable.

Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn 
P Pedersen (b...@mbg.au.dk). Deadline is July 31st 2021.

The city
In Aarhus you have easy access to beautiful nature and an exciting culture and 
city life that make Aarhus a wonderful place to live and work. See 
https://international.au.dk/life/locations/ for further details on the city and 
the university.



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