Re: [ccp4bb] tNCS incompatible with cell dimensions

[Boaz Shaanan]

Wouldn't c222 or c222(1) be included in the Phaser run if all orthorhombic sg's were requested?
Boaz

Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel



On May 31, 2019 23:37, Diana Tomchick  wrote:


Your native Patterson indicates pseudo C-centering. Are you sure you don’t have space group C222(1)?


If your space group is correct, it’s still pseudo C-centered. You should see that in the intensity-weighted reciprocal lattice.


You could try re-indexing on just the most intense spots to give you a data set indexed in a C-centered lattice. Use that data to solve via MR, then convert to the data indexed in the actual space group.


Diana



**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)


On May 31, 2019, at 3:09 PM, Kevin Jude  wrote:



Hello community, I wonder if I could solicit advice about a problematic dataset. I plan to solve the structure by molecular replacement and expect that the protein is relatively compact, ie not elongated. SAXS data supports this expectation.



The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2 with a = 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with 40% solvent. The native Patterson shows a large peak (12 sigma) suggesting a tNCS vector of {0.5,
 0.5, 0}.


If you're sharper than me, you may have already spotted the problem - c is the long axis of the unit cell, but tNCS constrains the proteins to a plane parallel to the a,b plane. Indeed, molecular replacement attempts using Phaser will not give
 a solution in any orthorhombic space group unless I turn off packing, and then I get large overlaps in the a,b plane and huge gaps along c.


Since I believe that my model is good (or at least the correct shape, based on SAXS), I wonder if I'm misinterpreting my crystallographic data. Any insights into how to approach this problem would be much appreciated.












--

Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute

Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: 
(650) 723-6431















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Re: [ccp4bb] tNCS incompatible with cell dimensions

[Diana Tomchick]

Your native Patterson indicates pseudo C-centering. Are you sure you don’t have 
space group C222(1)?

If your space group is correct, it’s still pseudo C-centered. You should see 
that in the intensity-weighted reciprocal lattice.

You could try re-indexing on just the most intense spots to give you a data set 
indexed in a C-centered lattice. Use that data to solve via MR, then convert to 
the data indexed in the actual space group.

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On May 31, 2019, at 3:09 PM, Kevin Jude 
mailto:kj...@stanford.edu>> wrote:

Hello community, I wonder if I could solicit advice about a problematic 
dataset. I plan to solve the structure by molecular replacement and expect that 
the protein is relatively compact, ie not elongated. SAXS data supports this 
expectation.

The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2 with a 
= 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with 40% 
solvent. The native Patterson shows a large peak (12 sigma) suggesting a tNCS 
vector of {0.5, 0.5, 0}.

If you're sharper than me, you may have already spotted the problem - c is the 
long axis of the unit cell, but tNCS constrains the proteins to a plane 
parallel to the a,b plane. Indeed, molecular replacement attempts using Phaser 
will not give a solution in any orthorhombic space group unless I turn off 
packing, and then I get large overlaps in the a,b plane and huge gaps along c.

Since I believe that my model is good (or at least the correct shape, based on 
SAXS), I wonder if I'm misinterpreting my crystallographic data. Any insights 
into how to approach this problem would be much appreciated.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431




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[ccp4bb] tNCS incompatible with cell dimensions

[Kevin Jude]

Hello community, I wonder if I could solicit advice about a problematic
dataset. I plan to solve the structure by molecular replacement and expect
that the protein is relatively compact, ie not elongated. SAXS data
supports this expectation.

The crystals diffract to 2.6 Å resolution and appear to be in P 21 21 2
with a = 49, b = 67, c = 94, which should fit <=2 molecules in the ASU with
40% solvent. The native Patterson shows a large peak (12 sigma) suggesting
a tNCS vector of {0.5, 0.5, 0}.

If you're sharper than me, you may have already spotted the problem - c is
the long axis of the unit cell, but tNCS constrains the proteins to a plane
parallel to the a,b plane. Indeed, molecular replacement attempts using
Phaser will not give a solution in any orthorhombic space group unless I
turn off packing, and then I get large overlaps in the a,b plane and huge
gaps along c.

Since I believe that my model is good (or at least the correct shape, based
on SAXS), I wonder if I'm misinterpreting my crystallographic data. Any
insights into how to approach this problem would be much appreciated.

--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431



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[ccp4bb] Network launch event: Interfaces in Cryo-EM (ICE) on July 3rd

[Jay Bertrand]

Hi All,
I wanted to signal the event on 'Interfaces in Cryo-EM (ICE)' that will be 
taking place at the Research Complex at Harwell (RCaH) in Didcot, U.K. on July 
3rd. A key goal of the meeting is to build a network for academic researchers 
interested in Cryo-EM and members of related Industry sectors (pharmaceutical, 
biotechnology, instrument). Please use the link at the bottom of this message 
if you would like to register.

Regards,
Jay


[https://gallery.mailchimp.com/e111d9da49c2dd9a729d32013/images/3cc69506-c70d-4f1a-a1a1-ee80bdf4acf0.jpg]

Network launch event: Interfaces in Cryo-EM (ICE)

Hosted by: Rosalind Franklin Institute / University of Oxford / Oxford BRC / 
Diamond

3 July 2019
9:30 to 17:00 - Rutherford Appleton Laboratory, Research Complex at Harwell

Vision:

  *   Build a community of academic researchers interested in Cryo-EM and 
members of related Industry sectors (pharmaceutical, biotechnology, 
instrument), to foster pre-competitive knowledge sharing, collaborations, and 
to promote investment in cryo-EM infrastructure and future applications
  *   Create a regular forum for discussion, with focus on new developments and 
technology
  *   Promote discussion workshops for networking and relationship building

Themes of the forum:

  *   Application of cryo-EM to life sciences and drug discovery
  *   Evolution of electron microscopy
  *   Single particle cryo-EM: protein science, cofactors (e.g. nanodiscs and 
nanobodies), grid prep, data analysis

Confirmed speakers:

  *   John Bell - Regius Professor of Medicine, Oxford University
  *   Dave Stuart - Life Sciences Director, Diamond Light Source
  *   Peijun Zhang - Director of the electron Bio-Imaging Centre (eBIC), 
Diamond Light Source
  *   Chris Russo - Group Leader, MRC Laboratory of Molecular Biology
  *   James Naismith - Director of The Rosalind Franklin Institute
  *   Ray Owens - Principal scientist, Rosalind Franklin Institute

To register and for event programme please click 
here


Best wishes,
The ICE Committee












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Re: [ccp4bb] Unknown density

[Nicholas Keep]

There is no blue (2fo-fc) density at least at the current contour level 
in your difference density.  That probably indicates what you are seeing 
is noise rather than a real feature.


I am also seeing more intense (above 7 sigma in some cases) positive 
difference density without actual density in my current refmac refined 
structure than I am used to.


I ascribed this to being in P1 with significant anisotropy leading to 
ripples???, but if this is widespread then there may have been tweaks to 
the software.  Anyone else want to comment on this


Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door



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[ccp4bb] PhD position at NUI Galway, Ireland

[Crowley, Peter]

PhD position at NUI Galway, Ireland


The Crowley laboratory is recruiting a PhD candidate to begin in September 
2019. This four year fully-funded project is part of SFI research centre 
SSPC-Pharm5, and includes an annual stipend, registration fees, consumables 
costs and travel allowance.


We are looking for a highly motivated PhD candidate with a passion for protein 
science. Applications are welcome from BSc or MSc graduates of Chemistry, 
Biochemistry or Biotechnology. Prior experience in protein purification is an 
advantage.


Controlled protein assembly provides a means to construct biocompatible, 
nanoscale devices and functional materials. We are interested in ligands that 
facilitate protein assembly and crystallization. Such “molecular glues” trigger 
assembly by providing a surface on which two or more proteins can associate. 
Macrocycles such as calixarenes and cucurbiturils are versatile "glues" for 
protein assembly and crystallization.[1-4] We have shown how 
sulfonato-calix[8]arene can control the assembly of lysine-rich cytochrome 
c.[3] Different types of assemblies were generated depending on the protein – 
calixarene ratio. While our work to date has focused on cationic proteins[1,4] 
now we will expand the scope to include neutral proteins. Our main interest is 
to discover methods of generating porous assemblies with potential applications 
in sensing and catalysis.


Applications to include:

- motivation statement (~500 words)

- 2 page CV

- contact details for 2 referees

- PDF of BSc or MSc thesis


Enquiries to peter.crow...@nuigalway.ie


References

1. McGovern RE, Fernandes H, Khan AR, Power NP, Crowley PB Protein camouflage 
in cytochrome c - calixarene complexes. Nature Chem. 2012, 4, 527-533.

2. Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale 
E, Crowley PB Cucurbit[7]uril-dimethyllysine recognition in a model protein. 
Angew. Chem. Int. Ed. Engl. 2018, 57, 7126-7130.

3. Rennie ML, Fox GC, Pérez J, Crowley PB Auto-regulated protein assembly on a 
supramolecular scaffold. Angew. Chem. Int. Ed. Engl. 2018, 57, 13764-13769.

4. Alex JM, Rennie ML, Engilberge S, Lehoczki G, Dorottya H, Fizil Á, Batta G, 
Crowley PB Calixarene-mediated assembly of a small antifungal protein. IUCrJ 
2019, 6, 238–247.


Prof. Peter Crowley

School of Chemistry

National University of Ireland, Galway

Ireland





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