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Department of Molecular and Cell Biology
The Institute of Materials Science
University of Connecticut
97 North Eagleville Road
Storrs, CT 06269-3136, USA
Phone:  +1 860 486 3830
Fax:      +1 860 486 4745
E-mail: peter.burkh...@uconn.edu<mailto:peter.burkh...@uconn.edu>
Web:    http://faculty.ims.uconn.edu/~pburkhard/

On 19 Sep 2016, at 19:01, CCP4BB automatic digest system 
<lists...@jiscmail.ac.uk<mailto:lists...@jiscmail.ac.uk>> wrote:

There are 10 messages totaling 22446 lines in this issue.

Topics of the day:

 1. Problem of diffraction patterns (2)
 2. How to determine the number of occurrences of a particular type of amino
    acid on the surface of a protein
 3. Teaching models and cognition w/ xtallography as example, high school lvl
    (2)
 4. multiple similar solutions in phaser (4)
 5. Job Posting - Research Fellow in Protein Crystallography - Portsmouth, UK
    (BBSRC/NSF)

----------------------------------------------------------------------

Date:    Mon, 19 Sep 2016 16:37:15 +0800
From:    "xiaoron...@cau.edu.cn<mailto:xiaoron...@cau.edu.cn>" 
<xiaoron...@cau.edu.cn<mailto:xiaoron...@cau.edu.cn>>
Subject: Problem of diffraction patterns

Dear all:
We have got two crystals in crystallization solution(crystal growth for more 
than a month):
11.25% PEG8000  0.625 M NaCl   0.15 M MgCl2   75 mM Tris-HCl pH8.5   33 mM Na/K 
phosphate pH6.2    final pH7.09
When we mounted the crystal to diffraction test, the diffract pattern is as 
follow picture shows:
The diffraction result is opened with HKL2000, the right section is magnified 
view of left black box.
It seems that there are a badly diffraction at about 9~12 Å.
Is there anyone knows why? Can we discern this is the crystal of protein or 
salt from the diffraction pattern?
If it is a protein crystal, have any suggestions for subsequent optimization of 
this protein crystals?

Best,
Xiaorong Li


xiaoron...@cau.edu.cn<mailto:xiaoron...@cau.edu.cn>

------------------------------

Date:    Mon, 19 Sep 2016 10:05:23 +0100
From:    Klaus Fütterer <k.futte...@bham.ac.uk>
Subject: Re: Problem of diffraction patterns

Dear Xiarong,

You appear to have diffraction from a salt crystal ( the highly intense spots 
at high resolution) mixed with something that may be protein (speckles of 
difraction spots at 9 - 12 Å), plus some diffraction from ice (rings from 3.7 Å 
outwards).

Klaus


=======================================================================

Dr. Klaus Fütterer
Deputy Head of School
Undergraduate Admissions
Room 717, Biosciences Tower

School of Biosciences  P: +44-(0)-121-414 5895
University of Birmingham          E: k.futte...@bham.ac.uk
Edgbaston                                      T: @KFbrumbio
Birmingham, B15 2TT, UK           W: http://tinyurl.com/futterer-lab
=======================================================================





On 19 Sep 2016, at 09:37, xiaoron...@cau.edu.cn <xiaoron...@cau.edu.cn> wrote:

Dear all:
We have got two crystals in crystallization solution(crystal growth for more 
than a month):
11.25% PEG8000  0.625 M NaCl   0.15 M MgCl2   75 mM Tris-HCl pH8.5   33 mM Na/K 
phosphate pH6.2    final pH7.09
When we mounted the crystal to diffraction test, the diffract pattern is as 
follow picture shows:
<Catch.jpg>
The diffraction result is opened with HKL2000, the right section is magnified 
view of left black box.
It seems that there are a badly diffraction at about 9~12 Å.
Is there anyone knows why? Can we discern this is the crystal of protein or 
salt from the diffraction pattern?
If it is a protein crystal, have any suggestions for subsequent optimization of 
this protein crystals?

Best,
Xiaorong Li
xiaoron...@cau.edu.cn <mailto:xiaoron...@cau.edu.cn>

------------------------------

Date:    Mon, 19 Sep 2016 12:14:10 +0200
From:    Gert Vriend <gerrit.vri...@radboudumc.nl>
Subject: Re: How to determine the number of occurrences of a particular type of 
amino acid on the surface of a protein

Hai Joel,

At the CMBI we maintain a series of protein structure (PDB-file based)
facilities at http://swift.cmbi.ru.nl/gv/facilities/. Robbie mentioned
the PDBFINDER2 already. One of the not so often used facilities is a
collection of 'lists' in which we performed some calculation or the
other over all PDB files.

Greetings
Gert

On 18-9-2016 16:08, Joel Sussman wrote:
  18-Sep-2016
Is there a simple way to determine (calculate) the number of occurrences of a 
particular type of amino acid on the surface of a protein,
e.g. How many Tyr are on the surface of a particular protein?
Any help, most appreciated.
Thanks
Joel
--------------------------------------------------------------------------------
Prof. Joel L. Sussman                              
joel.suss...@weizmann.ac.il<mailto:joel.suss...@weizmann.ac.il>   
www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel>
Dept. of Structural Biology   tel: +972  (8) 934 6309  
www.weizmann.ac.il/ISPC<http://www.weizmann.ac.il/ISPC>
Weizmann Institute of Science fax: +972  (8) 934 6312  
www.proteopedia.org<http://www.weizmann.ac.il/~joel>
Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
---------------------------------------------------------------------------------


Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het 
handelsregister onder nummer 41055629.
The Radboud university medical center is listed in the Commercial Register of 
the Chamber of Commerce under file number 41055629.

------------------------------

Date:    Mon, 19 Sep 2016 12:53:12 +0200
From:    Morten Grøftehauge <mortengroftehauge.w...@gmail.com>
Subject: Teaching models and cognition w/ xtallography as example, high school 
lvl

Hi everybody,

I am teaching a single 45 minute lesson about models in natural science in
a week long module on models and cognition. The students are in a science
high school, age approx. 17. I thought xtallography would be a good example
because it's very model-oriented, there's some stuff about validation and
model precision indicators (e.g. r-values), models that build on other
models (e.g. bond angles and lengths), data sharing vs not sharing etc.
They can open PyMol and see some electron density, and I can automate a lot
with scripts.

Now I've googled a bit and looked at the teaching resources at RCSB PDB 101
but I can't seem to find anything that helps with what I want to show them.
The guide to understanding PDB data looks like it has some useful things
but it's very practically oriented (
http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction).
What I need to teach is more meta.
*Does anyone know of any teaching resources that uses x-ray crystallography
models as a basis for talking about scientific models in general?*
If anyone has any great examples, specific structure-wise then please
mention them. But I may just use some of my own as examples.

Sincerely,
Morten

------------------------------

Date:    Mon, 19 Sep 2016 13:09:30 +0000
From:    Joel Sussman <joel.suss...@weizmann.ac.il>
Subject: Re: Teaching models and cognition w/ xtallography as example, high 
school lvl

19-Sep-2016
Dear Morten
Please consider looking at Proteopedia:  http://proteopedia.org, e.g. see:
* 3D molecular models: an introduction 
http://www.proteopedia.org/w/3D_Molecular_Models
* HIV-1 protease http://proteopedia.org/w/HIV-1_protease
* Group:SMART:A Physical Model of the β2-Adrenergic Receptor
http://www.proteopedia.org/w/Group:SMART:A_Physical_Model_of_the_%CE%B22-Adrenergic_Receptor
* Tutorial:How do we get the oxygen we breathe
http://proteopedia.org/w/Tutorial:How_do_we_get_the_oxygen_we_breathe
best regards,
Joel
--------------------------------------------------------------------------------
Prof. Joel L. Sussman                              
joel.suss...@weizmann.ac.il<mailto:joel.suss...@weizmann.ac.il>   
www.weizmann.ac.il/~joel<http://www.weizmann.ac.il/~joel>
Dept. of Structural Biology   tel: +972  (8) 934 6309  
www.weizmann.ac.il/ISPC<http://www.weizmann.ac.il/ISPC>
Weizmann Institute of Science fax: +972  (8) 934 6312  
www.proteopedia.org<http://www.weizmann.ac.il/~joel>
Rehovot 76100 ISRAEL          mob: +972 (50) 510 9600
---------------------------------------------------------------------------------

On 19Sep, 2016, at 13:53, Morten Grøftehauge 
<mortengroftehauge.w...@gmail.com<mailto:mortengroftehauge.w...@gmail.com>> 
wrote:

Hi everybody,

I am teaching a single 45 minute lesson about models in natural science in a 
week long module on models and cognition. The students are in a science high 
school, age approx. 17. I thought xtallography would be a good example because 
it's very model-oriented, there's some stuff about validation and model 
precision indicators (e.g. r-values), models that build on other models (e.g. 
bond angles and lengths), data sharing vs not sharing etc. They can open PyMol 
and see some electron density, and I can automate a lot with scripts.

Now I've googled a bit and looked at the teaching resources at RCSB PDB 101 but 
I can't seem to find anything that helps with what I want to show them. The 
guide to understanding PDB data looks like it has some useful things but it's 
very practically oriented 
(http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction). 
What I need to teach is more meta.
Does anyone know of any teaching resources that uses x-ray crystallography 
models as a basis for talking about scientific models in general?
If anyone has any great examples, specific structure-wise then please mention 
them. But I may just use some of my own as examples.

Sincerely,
Morten


------------------------------

Date:    Mon, 19 Sep 2016 16:48:00 +0100
From:    Abhishek Jalan <aa...@cam.ac.uk>
Subject: multiple similar solutions in phaser

Dear all,

I am trying to solve the structure of a collagen triple helix using phaser. The 
crystal diffracts to 2.0 A in P1 space group. Matthew's coefficient suggests 4 
molecules in the asu. When I tried to search for 5 components, phaser gave 8 
solutions each containing 4 triple helices.  The LLG scores are in the range of 
2200 and TFZ around 15.
All 8 solutions are similar except that the triple helices slide either up or 
down with respect to each other in different solutions.

Refinement of the top solution using default settings in phenix resulted in the 
following statistics.

                            start         final
 ---------------------------------------
 R-work:           0.5000        0.4003
 R-free:            0.4989        0.4586
 RMS(angles):      1.82            1.74
 RMS(bonds):     0.013          0.009

I am relatively new to crystallography and would appreciate any help in 
understanding why I am getting multiple solutions and if there is a way to 
reconcile the results into a single solution.

Thank you
Abhishek

------------------------------

Date:    Mon, 19 Sep 2016 16:54:37 +0100
From:    John McGeehan <john.mcgee...@port.ac.uk>
Subject: Job Posting - Research Fellow in Protein Crystallography - Portsmouth, 
UK (BBSRC/NSF)

Dear Colleagues,

We are looking for a Research Fellow with experience in structural biology
and/or biophysics/protein biochemistry to join us for a new UK-USA
BBSRC/NSF-funded project on the characterisation and engineering of novel
enzymes:

https://goo.gl/cr8rvU

Best Regards,
John
--
*Professor John McGeehan*
----------------------------------------------------------------------------------------------
Co-Director Institute of Biomedical and Biomolecular Science,
School of Biological Sciences,
University of Portsmouth,
King Henry Building,
PO1 2DY, UK
----------------------------------------------------------------------------------------------
Email: john.mcgee...@port.ac.uk
Web:   tinyurl.com/jmcgeehan
Lab:    tinyurl.com/mcgeehanlab
IBBS: tinyurl.com/IBBS-Portsmouth
Tel:    +44 (0) 2392 842042

------------------------------

Date:    Mon, 19 Sep 2016 16:09:47 +0000
From:    "Keller, Jacob" <kell...@janelia.hhmi.org>
Subject: Re: multiple similar solutions in phaser

This is a perfect case for potential static/statistical disorder. See

The 1.8 å crystal structure of a statically disordered 17 base-pair RNA duplex: 
principles of RNA crystal packing and its effect on nucleic acid structure
1 Sapan A Shah1, 2, Axel T Brunger1, 2,
http://dx.doi.org/10.1006/jmbi.1998.2385

To investigate/solve this, you should run Phaser-SAD using partial model 
phases, look for any anomalous atoms like Cl- or S, then auto rebuild to get 
the right registration. This will only work, however, if the crystal is not 
statically/statistically disordered. If it is, then you will see less-strong 
peaks at several registers, and you will have a tricky case on your hands.

JPK


-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Abhishek 
Jalan
Sent: Monday, September 19, 2016 11:48 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] multiple similar solutions in phaser

Dear all,

I am trying to solve the structure of a collagen triple helix using phaser. The 
crystal diffracts to 2.0 A in P1 space group. Matthew's coefficient suggests 4 
molecules in the asu. When I tried to search for 5 components, phaser gave 8 
solutions each containing 4 triple helices.  The LLG scores are in the range of 
2200 and TFZ around 15.
All 8 solutions are similar except that the triple helices slide either up or 
down with respect to each other in different solutions.

Refinement of the top solution using default settings in phenix resulted in the 
following statistics.

                            start         final
 ---------------------------------------
 R-work:           0.5000        0.4003
 R-free:            0.4989        0.4586
 RMS(angles):      1.82            1.74
 RMS(bonds):     0.013          0.009

I am relatively new to crystallography and would appreciate any help in 
understanding why I am getting multiple solutions and if there is a way to 
reconcile the results into a single solution.

Thank you
Abhishek

------------------------------

Date:    Mon, 19 Sep 2016 21:28:25 +0100
From:    Randy Read <rj...@cam.ac.uk>
Subject: Re: multiple similar solutions in phaser

Hi,

This is exactly what you’d expect to see with a repetitive structure.  One way 
or another, you have to figure out the sequence registration.  Jacob’s 
suggestion of SAD phases is great if you have any anomalous signal, but at this 
resolution you might see some good hints about side chain identities in maps 
phased with, say, a polyAla model.  As soon as you can reliably do 4-fold 
averaging, it should just drop out.

This is also the kind of thing that Arcimboldo is very good at, where the 
SHELXE density modification step will probably help a great deal.

Presumably you’re confident that it’s really P1 and not really a higher 
symmetry (as checked, for instance, with pointless or phenix.xtriage)?

Best wishes,

Randy

-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research    Tel: +44 1223 336500
Wellcome Trust/MRC Building                         Fax: +44 1223 336827
Hills Road                                                            E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.                               
www-structmed.cimr.cam.ac.uk

On 19 Sep 2016, at 16:48, Abhishek Jalan <aa...@cam.ac.uk> wrote:

Dear all,

I am trying to solve the structure of a collagen triple helix using phaser. The 
crystal diffracts to 2.0 A in P1 space group. Matthew's coefficient suggests 4 
molecules in the asu. When I tried to search for 5 components, phaser gave 8 
solutions each containing 4 triple helices.  The LLG scores are in the range of 
2200 and TFZ around 15.
All 8 solutions are similar except that the triple helices slide either up or 
down with respect to each other in different solutions.

Refinement of the top solution using default settings in phenix resulted in the 
following statistics.

                           start         final
---------------------------------------
R-work:           0.5000        0.4003
R-free:            0.4989        0.4586
RMS(angles):      1.82            1.74
RMS(bonds):     0.013          0.009

I am relatively new to crystallography and would appreciate any help in 
understanding why I am getting multiple solutions and if there is a way to 
reconcile the results into a single solution.

Thank you
Abhishek

------------------------------

Date:    Mon, 19 Sep 2016 20:58:30 +0000
From:    "Keller, Jacob" <kell...@janelia.hhmi.org>
Subject: Re: multiple similar solutions in phaser

Could this be as banal as having different origins in the different P1 
solutions?

Doesn't explain the poor refinement, though.

JPK


-----Original Message-----
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read
Sent: Monday, September 19, 2016 4:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] multiple similar solutions in phaser

Hi,

This is exactly what you’d expect to see with a repetitive structure.  One way 
or another, you have to figure out the sequence registration.  Jacob’s 
suggestion of SAD phases is great if you have any anomalous signal, but at this 
resolution you might see some good hints about side chain identities in maps 
phased with, say, a polyAla model.  As soon as you can reliably do 4-fold 
averaging, it should just drop out.

This is also the kind of thing that Arcimboldo is very good at, where the 
SHELXE density modification step will probably help a great deal.

Presumably you’re confident that it’s really P1 and not really a higher 
symmetry (as checked, for instance, with pointless or phenix.xtriage)?

Best wishes,

Randy

-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research    Tel: +44 1223 336500
Wellcome Trust/MRC Building                         Fax: +44 1223 336827
Hills Road                                                            E-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.                               
www-structmed.cimr.cam.ac.uk

On 19 Sep 2016, at 16:48, Abhishek Jalan <aa...@cam.ac.uk> wrote:

Dear all,

I am trying to solve the structure of a collagen triple helix using phaser. The 
crystal diffracts to 2.0 A in P1 space group. Matthew's coefficient suggests 4 
molecules in the asu. When I tried to search for 5 components, phaser gave 8 
solutions each containing 4 triple helices.  The LLG scores are in the range of 
2200 and TFZ around 15.
All 8 solutions are similar except that the triple helices slide either up or 
down with respect to each other in different solutions.

Refinement of the top solution using default settings in phenix resulted in the 
following statistics.

                           start         final
---------------------------------------
R-work:           0.5000        0.4003
R-free:            0.4989        0.4586
RMS(angles):      1.82            1.74
RMS(bonds):     0.013          0.009

I am relatively new to crystallography and would appreciate any help in 
understanding why I am getting multiple solutions and if there is a way to 
reconcile the results into a single solution.

Thank you
Abhishek

------------------------------

End of CCP4BB Digest - 18 Sep 2016 to 19 Sep 2016 (#2016-258)
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