URL: <http://gna.org/support/?3127> Summary: Opposite S2 values to expected Project: relax Submitted by: soumya__joseph Submitted on: Wed 05 Mar 2014 06:33:41 UTC Category: None Priority: 5 - Normal Severity: 3 - Normal Status: None Assigned to: None Originator Email: Open/Closed: Open Discussion Lock: Any Operating System: GNU/Linux _______________________________________________________ Details: Hi, I've conducted model-free analysis on relax using relaxation data (T1, T2 adn NOE) collected on 600 and 800 MHz instruments. I used the GUI with the default settings except for estimated rotational correlation time (for me it is 5 ns). My S2 order parameters are the inverse of what I expect. Disordered regions appear to have values closer to one and regions I know are structured have values that are closer to zero (see attached). The errors associated with the "ordered" NHs are quite large whereas those for dynamic residues are smaller. Here's what I observed. The calculation ran without any errors. It took about three days to run with a single processor. Is that normal or is there something wrong here? I have conducted consistency tests on these data. I guess I'd like to know what the threshold might be for something that has a Tc = 5 ns. My protein behaves as a single domain to the best of my knowledge. It is actually a tethered complex between two proteins but they bind each other. The dynamic region near the C-terminus is the glycine-serine loop that connects the two entities. I don't believe it comes apart very often as one of the proteins precipitates if left on its own. There appears to be no concentration-dependent dimerisation. The HSQC spectra of the protein at 0.04 and 0.6 mM look identical. The relaxation data for the 600 and 800 MHz exp are attached. The S2 has also been graphed. Does anyone know why my S2 parameters are the opposite to what I'm expecting? _______________________________________________________ File Attachments: ------------------------------------------------------- Date: Wed 05 Mar 2014 06:33:41 UTC Name: 800 rlx data.png Size: 78kB By: soumya__joseph T1, T2 and NOE relaxation data at 600 and 800 MHz and calculated S2 order parameters. <http://gna.org/support/download.php?file_id=20264> ------------------------------------------------------- Date: Wed 05 Mar 2014 06:33:41 UTC Name: relax600800_S2.png Size: 93kB By: soumya__joseph T1, T2 and NOE relaxation data at 600 and 800 MHz and calculated S2 order parameters. <http://gna.org/support/download.php?file_id=20265> _______________________________________________________ Reply to this item at: <http://gna.org/support/?3127> _______________________________________________ Message sent via/by Gna! http://gna.org/