Dear all
I am working on a structure that extends to about 2.5 A (CC* of 0.5) in the SG C 2221 (a=134.48, b=424.9, c=84.49). The long b axis is probably why the solvent content is 75 % with 2 NCS copies. The images were processed with XDS in Xia2.
After building and refining the model (Phenix+Refmac and one round of PDB_REDO), the Rwork/Rfree is about 34/39 %. Even the addition of water molecules does not change this, although only less than 10 molecules can be placed.
I ran Zanuda from the old GUI on my data and model - it suggests that the original SG is the correct one. I can easily see the density for my naturally-bound ligands (heme and iron-sulfur cluster), which makes me think the solution from Phaser run is indeed (almost) correct. The model statistics are also fairly good - Molprobity clashscore 37, RMSD angles 1.39, RMSD bonds 0.007, average B 90.4. Some loops have poor density, so I built them manually after superposing the NCS copies.
Is there a list of things that I should check to identify the source of the problem?
Thanks.
Mohamed
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