Hello everyone
I have some problems to analysis the xrd results to get the corresponding 3D structure of my protein with x'pert high score plus.
Does enyone have valuable suggestions?
Thanks
Hello Fatemeh Yaghoobiadeh
What protein you are referring to? To be analyzed by XRD and that this analysis will lead to a 3D structure, the protein must have a periodic structure. If it does, there must be some of this protein data structure in some database. So, the first step is to look for the possible structure you want to achieve. Then, one could do a Rietveld Refinement method, in order to determine if the pattern corresponds to that structure. Let me know if you need some help with this.
Best regards
Ricardo Tadeu
Hello Ricardo Tadeu Maia
This is a purified recombinant protein. What does your mean about the periodic structure? This protein is designed based on the deposited structures in public database. If it is possible for you, please let me know what should I do.
Sincerely
If you could show the XRD pattern and this deposited structure, we can try to do the comparison between your pattern and a theoretical pattern that can be calculated from the structure.
Hello Dear Richardo Tadeu Maia
Please find the attachment. deposited structure is 7Kfv.
If it is possible for you, please provide me a step-by-step manual to XRD analysis and get 3D structure of protein.
Dear Fatemeh Yaghoobiadeh
I was able to get the 3D structure from PBD database, I download the CIF file, but I was unable to get a XRD pattern of that structure, and the software VESTA is having trouble to calculate it. With most structures, I get a CIF file, put in VESTA, and it calculates a theoretical XRD powder pattern, but for this protein it's not working. Is this figure a XRD pattern? How did you get it? What I have been doing for years is to use softwares that can compare calculated XRD pattern (which is the one I am not finding) with the obtained XRD pattern. I have never done a refinement for a protein structure like this, but I am willing to learn and help with this.
Hello
Thanks for your response.
1. Does it mean that get its 3d structure is impossible?
2. Is it true or not: "In the case of protein, the use of reference xrd databases is not true.."
3. we only should compare the xrd pattern of the purified protein with the validated deposited structure?
4. What is the goal of protein Refinement ?
5. Yes,the figure is a diffrctogram presented by a reference laboratory for our purified protein.
I am very thankful
Hello
1- It's not impossible to determine the structure of the protein you obtained, but we would have to get some informations, like a theoretical powder pattern.
2 - The use of reference XRD powder is desirable, but I couldn't obtain until now.
3 - I am not an expert in proteins, but the comparison with a validated deposited structure is done to determine or confirm the structure of the one you synthesized.
4 - Refinement is a procedure to analyze XRD data. Once you have a validated structure, it must have a theoretical pattern. This pattern is compared to your obtained pattern. If the patterns match perfectly, you can say that you obtained the structure you wanted. If they don't match perfectly, which is more common, we have to do adjustments in the validated structure , to modify its pattern, and then match with the obtained pattern.
5 - So I think this is one possible path. Compare this structure with your obtained pattern.
Sincerely
Ricardo Tadeu
Hello
Thanks for your valuable information.
I downloaded more cof files from pdb to work and convert them to xrd pattern. However, the message of "bad cif file format" was appeared. I am working to resolve this issue.
Is it possible to share your email for further assistance?
Sincerely
Sure. I downloaded few CIF files and I couldn't calculated the powder patter. Lets keep in contact, I really want to find out how to do this procedure.
Best regards
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