Can't you break the ambiguity if there is significant anomalous signal? So,
you'd need to have collected data from a protein crystal with SeMet, or a heavy
atom, or near the S edge, and know the orientation of the crystal w.r.t. the
direction of the unique crystal axis (for instance from face
The difference between a rotamer with the possibility of 0% and an allowed
rotamer is sometimes not discernable by eye. I always try autofit rotamer in
Coot on this type of sidechain, and I often end up with something that, by
eye, fits the density as well as the original conformation and is
I'm glad George and Pavel have weighed in, since they're authorative figures.
I have another concern about the practice of using Fe2+ or Fe3+ scattering
factors for iron in a heme.
One thing small molecule crystallographers do is make sure they/we get F000
correct. This means that the number
On 06/26/2013 05:44 PM, Roberts, Sue A - (suer) wrote:
Hello Everyone
I have two data sets, from the same crystal form (space group P32)
of the same protein, collected at 100 K at SSRL, about 2.2 A
resolution, that refining to R = 0.14, Rf = 0.26 (refmac/TLS).
This is a molecular
Hello Everyone
I have two data sets, from the same crystal form (space group P32) of the same
protein, collected at 100 K at SSRL, about 2.2 A resolution, that refining to R
= 0.14, Rf = 0.26 (refmac/TLS). This is a molecular replacement solution, from
a model with about 40% homology (after
Hello
Actually, if the home source uses a copper tube, neither copper nor zinc have
much of an anomalous signal at that wavelength (the energy is below the
absorption edge for both).
The best way is to check the location of the absorption edge at the
synchrotron. Cu+ and Cu++ can be
Regarding suggestions that the pdb or the IUCR to tell us what to do:
IMO -
Neither of the usual solutions - (a) deleting side chains when there is no
density or (b) letting B factors go where they will - is without problems (this
is clear from the ongoing discussion). I would be really
I have used phaser to successfully solve a structure in P2x2x2x that had
pseudo-translational symmetry. It was unable to correctly choose the space
group, but after running phaser in all 8 possible space groups and inspecting
the best solutions in each the correct solution was clear.
Have you tried both the P43 and P41 space groups? I ask because you said you
got a solution in P43 but the likely space group is P4122. If the likely space
group is really P4122 (and not P4322), the corresponding space group is P41,
not P43.
Sue
On Feb 7, 2011, at 3:49 AM, Md. Munan Shaik
Have you tried acorn in ccp4? I've had it work well at this resolution,
especially if the protein/peptide has some alpha helical content. We used
acorn to solve a small cro protein that we couldn't get molecular replacement
to work with by using a 5-residue ideal poly-ala helix as the starting
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