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Questions tagged [xray-crystallography]

A method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions.

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Fusing two protein structures

I am trying to fuse a C-termiuns of one protein to an N-terminus of another. I do it in Discovery Studio by building tether and "align by tether". I tether oxygen of the carboxyl group with nitrogen ...
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Why do the most structurally well-characterized bacterial RNA polymerases belong to thermophiles?

From Lewin's Genes (11th edition, page 515): The only bacterial RNA polymerases for which high-resolution crystal structures have been solved, however, are from two thermophilic bacterial species, ...
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What is the fastest way to crystallise lysozyme (for student course)?

High school sudents are going to visit my university and I plan to demonstrate crystallisation of lysozyme. I ordered pure lysozyme from VWR. I can easily crystallise this within 15 min in batch (4% w/...
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Naming of Secondary Structure Elements

I have 2 questions regarding the naming of secondary structure elements ($\alpha$-helix and $\beta$-sheets), like helix C or sheet 2, which are often used in publications. Example protein: CYP1A2 ...
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NAG, FUC molecules in PDB files

In some proteins (such as 4ZXB, 6CE9 which are respectively apo and halo forms of insulin receptors), I see ligands such as FUC (ALPHA-L-FUCOSE) and NAG(N-Acetylglucosamine). No matter which paper I ...
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Generate mesh surface from protein structure

What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated. I'd prefer the output to be a ...
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Subset of Protein Crystal Structures (from PDB)

Is there a well-accepted subset of the Protein Data Bank set of protein structures that: Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural ...
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169 views

Techniques for detecting phosphorylation sites in proteins?

I would like to know how phosphorylated sites in proteins are detected in practice. I read some papers where the authors were talking about mass spectrometry techniques. But my question is that why ...
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Proteins in water vs proteins in crystal

I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays ...
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Resolution of X-ray crystallography

A structure determined by X-ray crystallography has a resolution of 1.5 Å. When I look at the coordinates, I find every backbone C-N distance is 1.32 Å.i.e. Accurately predicted. If resolution is not ...
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Determining the appropriate bioconjugate

I'm thinking of crosslinking two proteins. The crystallographic nature of the interaction and the binding motif for each molecule is know. The paper says the intermolecular contacts (over 50; van der ...
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Getting xyz co-ordinates from a .map file (CCP4 format) in VMD

I have a .map file which contains x-ray crystallography data of a bacteriophage. The format of the file is CCP4. I can open the file using VMD. However, I am unable to get the xyz co-ordinates. It ...
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Are original x-ray diffraction data available

Is it customary for investigators to publish the original x-ray diffraction data used in macromolecular structural determination? If not, why not; and if so, is there an online database where these ...
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Why are transmembrane proteins difficult to crystallise?

I know that in vivo there are a lot fewer transmembranous proteins in general, and that they are produced at a lower rate than their free counterparts. This is mainly because transmembrane proteins ...
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What are the benefits of elucidating the crystal structure of a protein?

I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we ...
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In the diffraction pattern of a protein crystal what exactly determines the intensities of the spots?

What I have read is that the contents of the unit cell affect the intensities, but how? I am also unclear on why you need to know the symmetry of the unit cell, what is that used for? I understand ...
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RMSD during conformational transition in proteins

When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved ...
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How does one calculate the resolution of a crystal structure?

Considering that I have a diffraction pattern of a crystal, how would I calculate the resolution of a structure in Angstroms? How does that value differ from the information that I would get from the ...
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Can protein structure be determined by X-Ray Diffraction in a single image?

I'm reading about the use of x-ray crystallography to determine protein structure. According to my book, data is collected at 30-360 angles (dependent on the symmetry of the protein). An illustration ...