Hmm maybe pseudosymmetry

No glaring issues like that or none that I could see. All different proteins from different labs and many (not all) have this oddity.

I wish we could follow this 2018 advice from Mr. Rupp : www.sciencedirect.com/science/arti... - "map inspection is the foundation of assessment " and " historic Table 1 will be relegated to the depths of supplemental material where it will be—in the author's opinion, rightfully—forgotten."

PS: all of the structures are absolutely gorgeous. Some have ligands. Its just that criteria such as Rfactors are often used as "quick, first glance metrics" to judge the agreement between the xray model vs. underlying data. So it would be good to have some sort of reason.

my own..

I think it’s due to their propensity to oligomerize even if their SEC shows predominantly monomers. Especially at higher concentrations. Most of the ones I have are beta strand swaps or at designed interfaces meant to bind a target (but appears to also have sticky propensity for itself)

Some examples. However density looks completely fine with no obvious defects.

As in dimer swapped? Those I have!

Calling all xray structure folks that have worked with denovo proteins. Do you suffer from high rfactors? Myself, someone else I know and now multiple structures all seem to suffer from this. Assuming we all tried our best in model building, what could be some causes?

Ohhh gotta convince some of the students I’m helping

The Critical Assessment of Structure Prediction (CASP) experiment is calling for prediction targets: Immune Complexes, Organic Ligand-Protein Complexes, Nucleic Acids and Complexes, Conformational Ensembles, Difficult Protein Structures and Complexes. Rule of Thumb: If AlphaFold3 can generate a high-quality model, it is likely not a CASP-grade challenge. If it struggles, we want it.

Is #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬

Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes.

The Rule of Thumb: If AF3 can’t model it, we want it.

Are there videos of previous wars?

Ive always been taught verbatim for decades that Glycines are helix breakers, but why is this protein filled of alpha helices so rich in glycines everywhere!

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two dist...

Bye bye dogma? www.science.org/doi/10.1126/...

In this case the denovo surface Asp is helping in coordination. I would say most denovo ones I’ve solved are heavily biased on the surface with D/E/K/R

Team just set up the tray!

Refined after adding the histidines, from both monomers of the assymetric unit. Very similar coordination spheres. If anyone is interested the tag is : GSGSHHWGSTHHHHHH. Dont ask me why it was designed that way 🙃 Im pretty sure the W is there to ensure absorbance at 280 nm

We cant be picky, we'll take whatever good protein to set up drops now. But I'll suggest the opposite approach if I dont see anything forming at first.

Oh I have told this user I would highly suggest doing their biochemistry again with uncleaved protein to avoid any suggestion that the tag mediates.

That’s my workflow now!

Alphafold and Autobuild also didnt help me :)

oh I can imagine. I took a few weeks away from this density and was like, ok the density is most likely NOT how I thought it is... I mean it looked like this! a big ball of density spaghetti. There was one Trp that did help (bottom left)

this lab doesnt cleave as it slows down throughput. and its usually His. But this is now the third case Ive seen for them that their tags make crystal contacts... However another lab that always cleaves, I never get crystals. I even got them to not cleave now 😆. But this lab I want them to cleave😝

refined without the metal yet, but condition has Li and Mg... I am betting on Mg though. Actually 4 of these contact sites as the unit cell contains 2 mols and both make similar structures (havent superimposed yet). Some of the sites I can even see bumps, likely h2o to complete the octa coordination

an xray density map depicting blue meshed density where an atomic model has been built.

Some people cleave tags religiously. This person didnt and made me solve their perfectly structured Histag. Probably also helped in packing. Might have to do experiments without it to show its not an artifact though.

Team cleave or not cleave?

I’m still running on a batch from 3 years ago… when you make mL and only use uL it takes a lot of time!

I think that’s the “scientific reasoning” we all use but I think no one has bothered to study it further until this elegant report! 😃

And sometimes it doesn’t even have to be disordered… SUMO the popular in fashion fusion also does not run true to size. Which confuses a whole lotta students! And it’s a ball!

I can finally stop cringing and sighing when I hear that sds-page separates only by size as most textbooks say

Thanks! I made the leap to Coot 1.X ever since the Tahoe update. I’m glad there are alot of changes at least compared to 2024. The home brew install also works seemlessly. I’m very excited that the Phenix devs may release their own build with Phenix itself too