puzzle picture
1384: Solved Foldit Design: Electron Density
Status: Closed

Summary

Name: 1384: Solved Foldit Design: Electron Density
Status: Closed
Created: 05/30/2017
Points: 100
Expired: 06/06/2017 - 23:00
Difficulty: Intermediate
Description: This puzzle features a protein designed from scratch by Foldit players! In Puzzle 1381 we asked players to try to predict the structure of this protein from the sequence alone. We have since solved the crystal structure of this protein, and here we are providing players with the refined electron density map. See the blog for more details. Players can load in solutions from Puzzle 1381 to see how their predictions fit in the electron density map, and players can try building into the electron density from an extended chain!

Sequence:
TELEKHREELKEFLKKEGITNVEIRIDNGRLEVRVEGGTERLKRFLEELRQKLEKKGYTVDIKIE
Categories: Electron Density, Overall, Prediction

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Comments

pauldunn's picture
User offline. Last seen 1 hour 54 min ago. Offline
Joined: 09/20/2010
Groups: Go Science
density puzzles still crashing on linux

Density puzzles still crashing on linux.

20170503-ce4d057080-linux_x64

https://fold.it/portal/node/2003463

https://fold.it/portal/node/2002859

bkoep's picture
User offline. Last seen 17 hours 56 min ago. Offline
Joined: 11/15/2012
Groups: None
Thanks for bumping the issue!

I know you've shared solutions for this crash on previous puzzles—if you also have a solution that crashes reproducibly on this puzzle and can Share with Scientists, that would be still helpful.

Or does Foldit crash when wiggling the start structure, immediately after opening the puzzle?

pauldunn's picture
User offline. Last seen 1 hour 54 min ago. Offline
Joined: 09/20/2010
Groups: Go Science
It will crash when wiggling

It will crash when wiggling the start structure, immediately after opening the puzzle. Let me know if I can provide any more information.

Wilm's picture
User offline. Last seen 6 weeks 6 days ago. Offline
Joined: 02/28/2013
Groups: Go Science
Resolution?

Just for (fun) reference, can you give us the resolution of the ED?

bkoep's picture
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Joined: 11/15/2012
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Resolution

This map has a resolution limit of 1.20 angstroms.

Wilm's picture
User offline. Last seen 6 weeks 6 days ago. Offline
Joined: 02/28/2013
Groups: Go Science
Resolution

Thanks. The number is a bit surprising to me if I compare that with the resolution of the previous puzzle 1357 at 1.5A. Puzzle 1384 has quite a few stretches of the protein that don't show up at all. I guess it makes sense if it is the maximum resolution this number is referring to...
So, if I read in a paper "the structure of protein x has been determined at 1.5A resolution" what does that mean exactly? On average 1.5A? Maximum of 1.5A? 1.5A except in variable regions? I know it is probably a bit pedantic, I just haven't thought about this much before Foldit ED puzzles.

bkoep's picture
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Joined: 11/15/2012
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Resolution limits

Good question! When we talk about resolution limits in x-ray crystallography, we're talking specifically about the extent of x-ray diffraction (see the blog for more on diffraction). With respect to the electron density map, the resolution limit is just that—a limit. A resolution limit of 1.5 Å means roughly that the raw data contain no information about positions closer than 1.5 Å.

Other effects can "blur" portions of the refined electron density map—mostly having to do with ambiguous atom placement (e.g. thermal motion, partial occupancy, disordered regions).

kabubi's picture
User offline. Last seen 6 weeks 5 days ago. Offline
Joined: 11/29/2008
Groups: Void Crushers
resolution

resolution of this puzzle appears lower than others to me.
i hardly recognize few residue.
It has been already trimmed?

Susume's picture
User is online Online
Joined: 10/02/2011
Why no cloud at protein surface?

It seems odd to see a cloud with very clear outlines for interior atoms and no cloud whatsoever for whole residues (not just sidechains) at the protein surface. I can imagine the many long blue sidechains on the surface of a foldit design being floppy and maybe not having cloud, but I would not expect the very short loops in this protein to be disordered, would you? The complete lack of cloud for a tyrosine is also surprising. What is going on?

Susume's picture
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Joined: 10/02/2011
Threshold is weird too

Another note - moving the threshold slider to the left usually shows more and more cloud, but in this puzzle a threshold of 0 shows the same as having it at a quarter of the slider - it's like the less-certain part of the cloud has been completely omitted.

bkoep's picture
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Joined: 11/15/2012
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Density Map

Hmm, that's strange. In the full electron density map, all of the residues (and most of the sidechains) are well resolved. Something must have happened when we trimmed the density map for the Foldit puzzle. I'm sorry we didn't catch that before posting the puzzle!

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons