date:20170206

[ccp4bb] Computational Crystallography Newsletter, Volume 8, Number 1

2017-02-06 Thread Nigel Moriarty

I am pleased to announce the publication of the latest issue of the
Computational Crystallography Newsletter:

   http://www.phenix-online.org/newsletter/

A listing of the articles and short communications is given below. Please
note that the newsletter accepts articles of a general nature of interest
to all crystallographers. Please send any articles to me at
nwmoria...@lbl.gov noting that there is a Word Template on the website to
streamline production.

January 2017 

Articles
- Deploying *cctbx.xfel* in Cloud Computing and High Performance Computing
Environments


Short Communications
- multi_core_run(), yet another simple tool for embarrassingly parallel jobs

- Phenix tool to compute a difference map for cryo-EM


Fitting tips #13 – O-pairs: The love-hate relationship of carboxyl oxygens


Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov

[ccp4bb] AW: [ccp4bb] How to determine the concentration of biotinylatedpeptide?

2017-02-06 Thread Hughes, Jon

very good point! you need lots of protein and it has to be pure (meaning also 
minimal buffer, salts and stuff) but it worked pretty well in our hands (when 
we were trying to measure the extinction coefficient of phytochrome). 
incidentally, I think that the notion of quantitative amino acid analysis being 
the gold standard is wrong. we had a sample analysed by different labs in 
different parts of the world – and the results varied by about 50%! maybe we 
were just unlucky, but maybe we won't be the only ones
best
jon

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nicholas 
Larsen
Gesendet: Montag, 6. Februar 2017 19:01
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] How to determine the concentration of biotinylated 
peptide?

These suggestions are all possible, but why not simply lyophilize it into a 
tared tube and weigh it out?

On Mon, Feb 6, 2017 at 12:28 PM, Alex Lee 
mailto:alexlee198...@gmail.com>> wrote:
Thank you all for your suggestions!

On Mon, Feb 6, 2017 at 5:53 AM, Artem Evdokimov 
mailto:artem.evdoki...@gmail.com>> wrote:
Hi,

In addition to HABA dye assay (which will work great but will also be fooled by 
any biotin that is not conjugated) you can do:

* quantitative MS
* TLC
* HPLC
* elemental analysis
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614710/ biotin catalysis of the 
N3- + I3- reaction (also fooled by free biotin of course)
* UV (but beware, biotin only absorbs strongly below 240nm so you're not super 
well off there

Artem
www.harkerbio.com
"all of our Biotin comes only from free-range gummy vitamin bears..."

- Cosmic Cats approve of this message

On Mon, Feb 6, 2017 at 2:03 AM, Debasish Kumar Ghosh 
mailto:dkgh...@cdfd.org.in>> wrote:
Hi Alex,

In addition to Mirella's suggestion I would like to make an addition which 
might be specifically useful for you. Since your peptide has biotin tag, You 
may use HABA dye assay for the exact quatifiation of biotin (and thus 
biotinylated peptide). As far I recall, Thermo scientific provide a kit for 
this assay. The assay is simple and gives accurate results.

Best !!!



Debasish

CSIR- Senior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA

Email(s): dkgh...@cdfd.org.in, 
dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html



- Original Message -
From: Alex Lee mailto:alexlee198...@gmail.com>>
To: CCP4BB@JISCMAIL.AC.UK
Sent: Mon, 06 Feb 2017 03:02:07 +0530 (IST)
Subject: [ccp4bb] How to determine the concentration of biotinylated peptide?

Dear All,

Sorry for the off-topic question, I'd like to do Biacore SPR assay with
N-terminal biotinylated peptide as ligand (to Biacore SA chip) and my
protein as analyte. I have a question of how to determine the concentration
of biotinylated peptide （synthetic peptide), if the peptide has no Tyr and
no Trp residue, I guess amino acid analysis may not work because the
N-terminal of the peptide is biotinylated.

I'd appreciate if anyone share his/her experience on this.




[This e-mail message may contain privileged, confidential and/or proprietary 
information of H3 Biomedicine. If you believe that it has been sent to you in 
error, please contact the sender immediately and delete the message including 
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contained therein. This e-mail message should not be interpreted to include a 
digital or electronic signature that can be used to authenticate an agreement, 
contract or other legal document, nor to reflect an intention to be bound to 
any legally-binding agreement or contract.]

[ccp4bb] Postdoctoral researcher in Structural Biology

2017-02-06 Thread Sebastian Deindl

Dear colleagues,


The Deindl group (www.deindl-lab.com) is recruiting 
a highly motivated postdoctoral researcher with a natural talent and strong 
motivation to identify and solve scientific problems. He/she will carry out 
cryo- EM or X-ray crystallographic and biochemical studies to study the 
mechanisms of chromatin-associated protein complexes in the framework of a 
recently awarded ERC grant.


The Deindl laboratory is an interdisciplinary group of scientists led by 
Assistant Professor Sebastian Deindl. The group combines an integrated 
structural biology (Cryo-EM, X-ray crystallography, XL-MS, SAXS) approach with 
single-molecule imaging (smFRET) to obtain a quantitative and mechanistic 
understanding of protein complexes involved in human disease states.

The postdoc will work in close collaboration with other structural biologists, 
biophysicists, and biochemists, but is expected to run his/her own project 
independently. A strong track record from experimental projects, a passion for 
science and good interpersonal skills are prerequisites for the position.

The researcher will benefit from access to state-of-the-art facilities for all 
relevant techniques. The SciLifeLab cryo-EM facility features state-of-the-art 
equipment, including a Titan Krios and Talos Arctica armed with the latest 
generation direct electron detectors and a modern computational infrastructure.

Please see http://deindl-lab.com/ for more information about the research in 
the Deindl lab.


APPLY ONLINE HERE: 
https://www.uu.se/en/about-uu/join-us/details/?positionId=134973

Re: [ccp4bb] How to determine the concentration of biotinylated peptide?

2017-02-06 Thread Nicholas Larsen

These suggestions are all possible, but why not simply lyophilize it into a
tared tube and weigh it out?

On Mon, Feb 6, 2017 at 12:28 PM, Alex Lee  wrote:

> Thank you all for your suggestions!
>
> On Mon, Feb 6, 2017 at 5:53 AM, Artem Evdokimov  > wrote:
>
>> Hi,
>>
>> In addition to HABA dye assay (which will work great but will also be
>> fooled by any biotin that is not conjugated) you can do:
>>
>> * quantitative MS
>> * TLC
>> * HPLC
>> * elemental analysis
>> * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614710/ biotin catalysis
>> of the N3- + I3- reaction (also fooled by free biotin of course)
>> * UV (but beware, biotin only absorbs strongly below 240nm so you're not
>> super well off there
>>
>> Artem
>> www.harkerbio.com
>> "all of our Biotin comes only from free-range gummy vitamin bears..."
>>
>> - Cosmic Cats approve of this message
>>
>> On Mon, Feb 6, 2017 at 2:03 AM, Debasish Kumar Ghosh > > wrote:
>>
>>> Hi Alex,
>>>
>>> In addition to Mirella's suggestion I would like to make an addition
>>> which might be specifically useful for you. Since your peptide has biotin
>>> tag, You may use HABA dye assay for the exact quatifiation of biotin (and
>>> thus biotinylated peptide). As far I recall, Thermo scientific provide a
>>> kit for this assay. The assay is simple and gives accurate results.
>>>
>>> Best !!!
>>>
>>>
>>>
>>> Debasish
>>>
>>> CSIR- Senior Research Fellow (PhD Scholar)
>>> C/o: Dr. Akash Ranjan
>>> Computational and Functional Genomics Group
>>> Centre for DNA Fingerprinting and Diagnostics
>>> Hyderabad, INDIA
>>>
>>> Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
>>> Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
>>> Lab URL: http://www.cdfd.org.in/labpages/computational_functional_gen
>>> omics.html
>>>
>>>
>>>
>>> - Original Message -
>>> From: Alex Lee 
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Sent: Mon, 06 Feb 2017 03:02:07 +0530 (IST)
>>> Subject: [ccp4bb] How to determine the concentration of biotinylated
>>> peptide?
>>>
>>> Dear All,
>>>
>>> Sorry for the off-topic question, I'd like to do Biacore SPR assay with
>>> N-terminal biotinylated peptide as ligand (to Biacore SA chip) and my
>>> protein as analyte. I have a question of how to determine the
>>> concentration
>>> of biotinylated peptide （synthetic peptide), if the peptide has no Tyr
>>> and
>>> no Trp residue, I guess amino acid analysis may not work because the
>>> N-terminal of the peptide is biotinylated.
>>>
>>> I'd appreciate if anyone share his/her experience on this.
>>>
>>
>>
>

-- 
[This e-mail message may contain privileged, confidential and/or 
proprietary information of H3 Biomedicine. If you believe that it has been 
sent to you in error, please contact the sender immediately and delete the 
message including any attachments, without copying, using, or distributing 
any of the information contained therein. This e-mail message should not be 
interpreted to include a digital or electronic signature that can be used 
to authenticate an agreement, contract or other legal document, nor to 
reflect an intention to be bound to any legally-binding agreement or 
contract.]

Re: [ccp4bb] How to determine the concentration of biotinylated peptide?

2017-02-06 Thread Alex Lee

Thank you all for your suggestions!

On Mon, Feb 6, 2017 at 5:53 AM, Artem Evdokimov 
wrote:

> Hi,
>
> In addition to HABA dye assay (which will work great but will also be
> fooled by any biotin that is not conjugated) you can do:
>
> * quantitative MS
> * TLC
> * HPLC
> * elemental analysis
> * https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614710/ biotin catalysis
> of the N3- + I3- reaction (also fooled by free biotin of course)
> * UV (but beware, biotin only absorbs strongly below 240nm so you're not
> super well off there
>
> Artem
> www.harkerbio.com
> "all of our Biotin comes only from free-range gummy vitamin bears..."
>
> - Cosmic Cats approve of this message
>
> On Mon, Feb 6, 2017 at 2:03 AM, Debasish Kumar Ghosh 
> wrote:
>
>> Hi Alex,
>>
>> In addition to Mirella's suggestion I would like to make an addition
>> which might be specifically useful for you. Since your peptide has biotin
>> tag, You may use HABA dye assay for the exact quatifiation of biotin (and
>> thus biotinylated peptide). As far I recall, Thermo scientific provide a
>> kit for this assay. The assay is simple and gives accurate results.
>>
>> Best !!!
>>
>>
>>
>> Debasish
>>
>> CSIR- Senior Research Fellow (PhD Scholar)
>> C/o: Dr. Akash Ranjan
>> Computational and Functional Genomics Group
>> Centre for DNA Fingerprinting and Diagnostics
>> Hyderabad, INDIA
>>
>> Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
>> Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
>> Lab URL: http://www.cdfd.org.in/labpages/computational_functional_
>> genomics.html
>>
>>
>>
>> - Original Message -
>> From: Alex Lee 
>> To: CCP4BB@JISCMAIL.AC.UK
>> Sent: Mon, 06 Feb 2017 03:02:07 +0530 (IST)
>> Subject: [ccp4bb] How to determine the concentration of biotinylated
>> peptide?
>>
>> Dear All,
>>
>> Sorry for the off-topic question, I'd like to do Biacore SPR assay with
>> N-terminal biotinylated peptide as ligand (to Biacore SA chip) and my
>> protein as analyte. I have a question of how to determine the
>> concentration
>> of biotinylated peptide （synthetic peptide), if the peptide has no Tyr and
>> no Trp residue, I guess amino acid analysis may not work because the
>> N-terminal of the peptide is biotinylated.
>>
>> I'd appreciate if anyone share his/her experience on this.
>>
>
>

[ccp4bb] Employment opportunities at Charles River Labs

2017-02-06 Thread Leonard, Philip

Dear colleagues,

I would like to draw your attention to the following employment opportunities 
within Charles River Labs' Structural Biology group, based in Saffron Walden, 
UK:

https://jobs.criver.com/job/saffron-walden/protein-crystallographer/4665/3817382

https://jobs.criver.com/job/saffron-walden/senior-protein-scientist/4665/3928074

https://jobs.criver.com/job/saffron-walden/protein-scientist/4665/3817383

Best regards,

Phil.


Philip Leonard, PhD
Team Leader, Structural Biology | Charles River
Chesterford Research Park, CB10 1XL, United Kingdom
P: +44 1799 532601
philip.leon...@crl.com | 
www.criver.com
LinkedIn | 
Twitter | 
Facebook | 
Eureka

Discovery from Charles River helps you take the right steps, at the right time, 
to reach each milestone on your journey through drug development. Let's move 
forward together.

[ccp4bb] Position available for crystallographer with Bruker AXS – Business Development Scientist Structural Biology

2017-02-06 Thread Vernon Smith

Dear CCP4 community,

A position is available for an experienced crystallographer to join Bruker AXS 
in a scientific support role in the Structural Biology Business.  The 
successful candidate will join a highly motivated team, providing scientific 
and application support in the fields of macromolecular crystallography and 
biological SAXS. The candidate will contribute to the development and 
implementation of new hardware and software, provide specialist sales and 
application support, conduct customer trainings and support product marketing.

Location Karlsruhe, Germany
Full-time, permanent

Main duties

•   Supporting sales activities by determining potential customers needs 
through technical consultation
•   Planning and conducting instrument demonstrations to potential 
customers and reporting of results
•   Providing customer training and support
•   Writing technical application notes and other marketing materials
•   Critically testing and evaluating new technologies and software
•   Presentation of new technologies and scientific results at conferences

Experience and skills

We are looking for a candidate with the following strengths –

•   Master or PhD in Biochemistry, Chemistry, Molecular Biology or similar
•   significant experience in protein structure determination using X-ray 
crystallography and or SAXS
•   Results driven with the ability to manage projects and deadlines
•   Good technical and troubleshooting skills
•   Fluent in written and spoken English 
•   Willingness to travel both within Europe and worldwide for a 
significant amount of time(20 -40% working time)

Preference will be given to applicants with experience in the use and 
maintenance of X-ray systems, experience in customer/user support or teaching, 
and a high level of aptitude in X-ray diffraction instrumentation and methods.

Interested candidates may submit their applications through Bruker’s Careers 
Portal at https://www.bruker.com/about-us/career.html 

Alternatively, further information can be obtained by contacting:

Vernon Smith PhD
Business Development Manager – Structural Biology
Bruker AXS
vernon.sm...@bruker.com

[ccp4bb] PhD position available - PDZ-net european training program

2017-02-06 Thread Apirat Chaikuad

Posted on behalf on Prof. Stefan Knapp.

We currently have a PhD position available within Prof. Stefan Knapp group at 
Goethe-university Frankfurt:

The project is embedded into a highly interactive European training program 
involving internationally well recognized laboratories and companies.  The 
advertised position aims to study the function and structure of modular 
proteins that organize multiple PDZ domains into supramodules. We will study 
the structure and substrate specificity of these multi-domain assemblies with 
the goal to elucidate their function in cellular signalling and to exploit the 
possibility for the development of protein interaction inhibitors targeting PDZ 
supramodules.

https://www.uni-frankfurt.de/53541648/Stellenausschreibungen

The candidate should have a background in protein biochemistry, and MUST not 
have resided or carried out his/her main activity in GERMANY (not DENMARK as 
wrongly written in the website linked above) for more than 12 months during the 
last 3 years immediately prior to the recruitment.

The post is available immediately.

Anyone interested in the post, please send their CV to Prof. Stefan Knapp (see 
email in the link above). The formal closing date is on Friday 17th February 
2017. (but a few day late application might be considered).

Best,
Prof. Stefan Knapp

Re: [ccp4bb] How to determine the concentration of biotinylated peptide?

2017-02-06 Thread Artem Evdokimov

Hi,

In addition to HABA dye assay (which will work great but will also be
fooled by any biotin that is not conjugated) you can do:

* quantitative MS
* TLC
* HPLC
* elemental analysis
* https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614710/ biotin catalysis of
the N3- + I3- reaction (also fooled by free biotin of course)
* UV (but beware, biotin only absorbs strongly below 240nm so you're not
super well off there

Artem
www.harkerbio.com
"all of our Biotin comes only from free-range gummy vitamin bears..."

- Cosmic Cats approve of this message

On Mon, Feb 6, 2017 at 2:03 AM, Debasish Kumar Ghosh 
wrote:

> Hi Alex,
>
> In addition to Mirella's suggestion I would like to make an addition which
> might be specifically useful for you. Since your peptide has biotin tag,
> You may use HABA dye assay for the exact quatifiation of biotin (and thus
> biotinylated peptide). As far I recall, Thermo scientific provide a kit for
> this assay. The assay is simple and gives accurate results.
>
> Best !!!
>
>
>
> Debasish
>
> CSIR- Senior Research Fellow (PhD Scholar)
> C/o: Dr. Akash Ranjan
> Computational and Functional Genomics Group
> Centre for DNA Fingerprinting and Diagnostics
> Hyderabad, INDIA
>
> Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
> Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
> Lab URL: http://www.cdfd.org.in/labpages/computational_
> functional_genomics.html
>
>
>
> - Original Message -
> From: Alex Lee 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Mon, 06 Feb 2017 03:02:07 +0530 (IST)
> Subject: [ccp4bb] How to determine the concentration of biotinylated
> peptide?
>
> Dear All,
>
> Sorry for the off-topic question, I'd like to do Biacore SPR assay with
> N-terminal biotinylated peptide as ligand (to Biacore SA chip) and my
> protein as analyte. I have a question of how to determine the concentration
> of biotinylated peptide （synthetic peptide), if the peptide has no Tyr and
> no Trp residue, I guess amino acid analysis may not work because the
> N-terminal of the peptide is biotinylated.
>
> I'd appreciate if anyone share his/her experience on this.
>

Re: [ccp4bb] !SPAM: [ccp4bb] P622 xds index process with large unit cell

2017-02-06 Thread Tim Gruene

Dear Peter,

if this is indeed your entire XDS.INP, you asked XDS to refine all parameters 
except the axis during the integration step. This may have led to a drifting 
away from the input parameters. Try e.g.

REFINE(INTEGRATE)=CELL ORIENTATION BEAM

to fix the detector distance during integration.

How did XDS index the data, did it come up with the same unit cell parameters?

Best,
Tim

On Monday 06 February 2017 10:31:43 AM peter66 wright wrote:
> Dear All,
> 
> I got a data set from Diamond recently with space group of P622 and  cell
> parameters: 87 87 629; 90 90 120.
> I can process the data using mosflm at home, However, XDS could not do with
> error saying " !!! ERROR !!! CANNOT INTERPRETE LATTICE BY THE GIVEN UNIT
> CELL".
> Can anyone advice me how to change the XDS.INP parameters so that I can
> process the data using xds? Below is the XDS.INP
> 
> !JOB=IDXREF DEFPIX XPLAN INTEGRATE CORRECT
> JOB=DEFPIX INTEGRATE CORRECT
> ! The definition of OVERLOAD= should be read from the image
> ! header really...
> 
> DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=1048500
> CORRECTIONS=ALL
> DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
> DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
> TRUSTED_REGION=0.0 1.41
> SENSOR_THICKNESS=0.32000
> 
> ! Do we need these? In the first pass, assume so...
> UNTRUSTED_RECTANGLE= 487  495 0 2528
> UNTRUSTED_RECTANGLE= 981  989 0 2528
> UNTRUSTED_RECTANGLE=1475 1483 0 2528
> UNTRUSTED_RECTANGLE=1969 1977 0 2528
> UNTRUSTED_RECTANGLE=   0 2464   195  213
> UNTRUSTED_RECTANGLE=   0 2464   407  425
> UNTRUSTED_RECTANGLE=   0 2464   619  637
> UNTRUSTED_RECTANGLE=   0 2464   831  849
> UNTRUSTED_RECTANGLE=   0 2464  1043 1061
> UNTRUSTED_RECTANGLE=   0 2464  1255 1273
> UNTRUSTED_RECTANGLE=   0 2464  1467 1485
> UNTRUSTED_RECTANGLE=   0 2464  1679 1697
> UNTRUSTED_RECTANGLE=   0 2464  1891 1909
> UNTRUSTED_RECTANGLE=   0 2464  2103 2121
> UNTRUSTED_RECTANGLE=   0 2464  2315 2333
> 
> MAXIMUM_NUMBER_OF_PROCESSORS=16
> NY=2527 NX=2463 QX=0.17200 QY=0.17200
> ORGX=1215.3 ORGY=1291.5
> ROTATION_AXIS= 1.0 0.0 0.0
> DETECTOR_DISTANCE=658.54
> X-RAY_WAVELENGTH=0.979500
> OSCILLATION_RANGE=0.200
> INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
> FRACTION_OF_POLARIZATION=0.99
> POLARIZATION_PLANE_NORMAL=0.0 1.0 0.0
> FRIEDEL'S_LAW=FALSE
> NAME_TEMPLATE_OF_DATA_FRAMES=/users/.../susan1_240/ProplexG1_1_.cbf
> STARTING_ANGLE=-110.000 STARTING_FRAME=1
> INCLUDE_RESOLUTION_RANGE=30.00 3.1
> UNIT_CELL_CONSTANTS=87.31 87.31 629.62 90.00 90.00 120.00
> SPACE_GROUP_NUMBER=178
> MAX_FAC_Rmeas=3.0
> DATA_RANGE=1 240
> 
> **
> 
> Thanks for help.
-- 
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
Principal Investigator
Biology and Chemistry
OFLC/102
CH-5232 Villigen PSI

Phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A



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[ccp4bb] P622 xds index process with large unit cell

2017-02-06 Thread peter66 wright

Dear All,

I got a data set from Diamond recently with space group of P622 and  cell
parameters: 87 87 629; 90 90 120.
I can process the data using mosflm at home, However, XDS could not do with
error saying " !!! ERROR !!! CANNOT INTERPRETE LATTICE BY THE GIVEN UNIT
CELL".
Can anyone advice me how to change the XDS.INP parameters so that I can
process the data using xds? Below is the XDS.INP

!JOB=IDXREF DEFPIX XPLAN INTEGRATE CORRECT
JOB=DEFPIX INTEGRATE CORRECT
! The definition of OVERLOAD= should be read from the image
! header really...

DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=1048500
CORRECTIONS=ALL
DIRECTION_OF_DETECTOR_X-AXIS= 1.0 0.0 0.0
DIRECTION_OF_DETECTOR_Y-AXIS= 0.0 1.0 0.0
TRUSTED_REGION=0.0 1.41
SENSOR_THICKNESS=0.32000

! Do we need these? In the first pass, assume so...
UNTRUSTED_RECTANGLE= 487  495 0 2528
UNTRUSTED_RECTANGLE= 981  989 0 2528
UNTRUSTED_RECTANGLE=1475 1483 0 2528
UNTRUSTED_RECTANGLE=1969 1977 0 2528
UNTRUSTED_RECTANGLE=   0 2464   195  213
UNTRUSTED_RECTANGLE=   0 2464   407  425
UNTRUSTED_RECTANGLE=   0 2464   619  637
UNTRUSTED_RECTANGLE=   0 2464   831  849
UNTRUSTED_RECTANGLE=   0 2464  1043 1061
UNTRUSTED_RECTANGLE=   0 2464  1255 1273
UNTRUSTED_RECTANGLE=   0 2464  1467 1485
UNTRUSTED_RECTANGLE=   0 2464  1679 1697
UNTRUSTED_RECTANGLE=   0 2464  1891 1909
UNTRUSTED_RECTANGLE=   0 2464  2103 2121
UNTRUSTED_RECTANGLE=   0 2464  2315 2333

MAXIMUM_NUMBER_OF_PROCESSORS=16
NY=2527 NX=2463 QX=0.17200 QY=0.17200
ORGX=1215.3 ORGY=1291.5
ROTATION_AXIS= 1.0 0.0 0.0
DETECTOR_DISTANCE=658.54
X-RAY_WAVELENGTH=0.979500
OSCILLATION_RANGE=0.200
INCIDENT_BEAM_DIRECTION=0.0 0.0 1.0
FRACTION_OF_POLARIZATION=0.99
POLARIZATION_PLANE_NORMAL=0.0 1.0 0.0
FRIEDEL'S_LAW=FALSE
NAME_TEMPLATE_OF_DATA_FRAMES=/users/.../susan1_240/ProplexG1_1_.cbf
STARTING_ANGLE=-110.000 STARTING_FRAME=1
INCLUDE_RESOLUTION_RANGE=30.00 3.1
UNIT_CELL_CONSTANTS=87.31 87.31 629.62 90.00 90.00 120.00
SPACE_GROUP_NUMBER=178
MAX_FAC_Rmeas=3.0
DATA_RANGE=1 240

**

Thanks for help.

Re: [ccp4bb] on the resoution of crystal

2017-02-06 Thread Joel Sussman

6-Feb-2017
Dear Pavel & Tim,
For a very good visualization & description of “Resolution”,
please see the Proteopedia page created primarily by Eric Martz at:
http://www.proteopedia.org/w/Resolution
it includes a pointer to James Holton’s movie showing an Electron Density Map 
vs. Resolution (with model overlay) going from 0.5Å to 5.Å resolution.
best regards
Joel


Prof. Joel L. Sussman  
joel.suss...@weizmann.ac.il   
www.weizmann.ac.il/~joel
Dept. of Structural Biology   tel: +972  (8) 934 6309  
www.proteopedia.org
Weizmann Institute of Science fax: +972  (8) 934 6312
Rehovot 76100 ISRAEL  mob: +972 (50) 510 9600
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On 5Feb, 2017, at 23:44, Tim Gruene 
mailto:tim.gru...@psi.ch>> wrote:

Dear Pavel,

I believe words have a meaning, but they are not defined. This may make
languages a little more demanding than mathematics, since you have to deal
with a variety of a few hundred thousand to millions, depending how popular
the language in question is, but personally I enjoy the challenge.

W.r.t. the thread, 3.8A resolution is poorer than 1.8A. I understand this is
what John meant to clarify.

Best,
Tim

On Sunday, February 5, 2017 11:12:10 AM CET Pavel Afonine wrote:
Hi Tim, hi Natesh,

one expression is mathematically, the other one is technically 'more

correct'.
I favour the terms poor and good resolution to avoid confusion, or
explicitly
list the values.

just out of curiosity.. what's your definition of 'poor' and 'good'
resolutions? I suspect there are as many definitions as many subscribers to
this list are -;)

One way to quantify resolution is that what kind of detail you can see in
the map, like for example:

- deformation density (~0.7A and higher) = ultra-high, sub-atomic,
sub-Angstrom;
- H atoms (~0.9A and higher) = not sure what the name is;
- individual non-H atoms (~1.2A and higher) = atomic;
- hole in rings (~2A and higher?) = high;
- medium;
- still can see side chains (up to 4.5A);
- no side-chains but SS elements (such as tubes of density for helices) =
low
- no SS, molecular envelopes = very low.

Note, resolution alone is not a good measure though. Data completeness is
similarly important, e.g. a map corresponding to 2A resolution may look
like a 3ish A resolution if you miss some low-resolution data or
high-resolution end is severely incomplete (Acta Cryst. (2014). D70,
2593-2606).

Low resolution  --> worse than 2.7 A

Ultra high resolution --> better than 0.95 A

Looking into this in some systematic way one can define low-resolution as
6A and lower, and ultra-high resolution as 0.7A and higher (Page 1291: Acta
Cryst. (2009). D65, 1283–1291).

All the best,
Pavel

--
--
Paul Scherrer Institut
Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297

GPG Key ID = A46BEE1A

[ccp4bb] AW: [ccp4bb] Unknown blob extended from catalytic serine residue

2017-02-06 Thread Herman . Schreuder

Dear Sharifah,

Was no protease inhibitor used during crystallization, or during the whole 
purification process? E.g. when a protease inhibitor cocktail was added during 
cell-lysis, a protease inhibitor may irreversibly have modified your serine.

If your protein is a protease, it may have reacted with a random peptide during 
purification and the modified protein may have selectively crystallized. In 
this case I would try to fit a few Ala residues as an acyl-intermediate, or 
even as a tetrahedral intermediate as the electron density seems to suggest, 
refine and see what side chains would fit best. You may also try mass-spec to 
get some information on the nature of your modification.

Good luck!
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von sharifah 
nur hidayah syed mazlan
Gesendet: Samstag, 4. Februar 2017 16:03
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [ccp4bb] Unknown blob extended from catalytic serine residue

Dear All,

I am working on a structure with an unknown blob extended from the gamma O of 
the catalytic serine residue. The resolution of the dataset is 1.38 A. I have 
no idea whether the residue is modified or the blob belongs to other molecule.

The protein was expressed in Rosettagami (DE3), purified using Ni-Sepharose 
(affinity chromatography) and Q-Sepharose (Anion exchange chromatography). The 
crystallization formulation used contain 15% PEG 8000, 0.2 M Ammonium sulphate, 
0.1 M sodium cacodylate trihydrate pH 6.5; and the buffer composed of 50 mM 
Sodium chloride and Phosphate buffer pH 8. No protease inhibitor was used (eg: 
PMSF)

I have tried to fit in diethylene glycol as shown in one of the attached 
figures, but as observed, it is not really fit and the molecule is in incorrect 
conformation.

Kindly help me with this matter.



Thanks and regards,

Sharifah Nur Hidayah
Universiti Putra Malaysia,
Malaysia

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