Hi, I cannot tell you how to make density better. However, you can verify if the substrate is in by anomalous signal if you can replace an atom in you substrate, or add one to it with the absorption edge in synchrotron-tunable energy range. In any case, you should keep in mind that depending on you compound and its binding nature to the protein, it may be sitting in many orientations and in many conformations. If this is true, it will be next to impossible to see all of it even at much higher resolutions than yours. Good luck, N.
Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> ________________________________ From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of yang li Sent: Tuesday, April 15, 2008 9:56 AM To: [email protected] Subject: [ccp4bb] Low resolution data with substrate Hi All, We have several substrate-soaked data with resoltuion from 3.1~3.6A, after refinement with the native structure, the rfree are in the range of 0.29~0.34. We found in the expected active site there do have extra densities, but not very clear. In some chains the densities are big while in other chains very small. For some good extra densities can fit the substrate in but cannot specify the accurate atom positions. And the map densities seem not very convictive(low resolution or bad refinement?). This is a relative big structure, I think it would be difficult to rebuild it in such low resolution. We also has tried to use the sulfur anomalous signal in the substrate in 1.54A, but it failed since all the sulfurs in the model have no signal. So anyone has some methods to make the density better or make sure whether it has substrate soaked in? Thanks!
