Hi Prem,
The first thing I would do is to make certain that you really have prot+DNA
crystals, and not DNA alone. If you can isolate enough crystals (you may need
15 or 30, depending on how large they are), SDS page would be informative. Run
protein and DNA alone and together in the same gel as
But what about the issue of resolution? As was previously pointed out, at say
3.2 Å resolution, many side chains will fail to fit, but it doesn't seem
appropriate to trim them all down. The users need to also be aware of the
quality/resolution of the structures that they are looking at.
Greg
Hi all,
I'm building a ~1.9Å structure that has a few Mg++ ions bound. I thought that
the expected distance for Mg-O was 2.1Å, but in refmac the default to Asp/Glu
oxygens appears to be 1.91 Å. Strangely, for a Mg-bound pyruvate ligand, the
default distance to one oxygen is 2.18 Å, but 1.91 Å f
Can anyone give examples of proteins that bind to DNA/RNA non-specifically? In
particular I'm interested in examples where interactions are limited to the
phosphate backbone, and not with bases. If you could email me off-list, I can
compile a summary for others that may be interested.
Thanks!
G
I have a question about the bond angle restraints in the DNA cif files. I
recently submitted a protein-DNA complex to the PDB, and found out that many of
the glycosidic bond angles (atoms O4'-C1'-N9/N1) were outside the accepted
range. I switched from CCP4 6.1.13 to 6.2.0 (installed/updated with
ght the DT (renamed Td) were
somehow "DY". By just deleting these MODRES lines it was fine.
On Sep 14, 2011, at 7:10 PM, Gregory Bowman wrote:
> I'm running into some geometry problems with my DNA model after refinement
> with refmac (version 5.5.0109), and would appreciate any
I'm running into some geometry problems with my DNA model after refinement with
refmac (version 5.5.0109), and would appreciate any feedback.
The problem is that the angles for many of the glycosidic bonds are 2 to 4
degrees off of the ideal values, and so are several standard deviations outsid
Hi all,
We have several primitive monoclinic datasets for the same protein with various
ligands, with essentially the same unit cell parameters. We would like to have
these with the molecules/density oriented the same way for easy comparison, but
as chance would have it, some have effectively
Hi all,
I have a large disordered loop (33aa) for a 2.0 Å dataset for which the rest of
the structure is well-defined, and phases are decent (Rwork=19.6, Rfree=24.6).
I can see some broken up density at one end, but have been unable to
convincingly build into into this region manually. I would
Krishan,
Here is a simple stand-alone python script that should do what you want.
Greg
#!/usr/bin/python
#
# rechainpdb.py
# usage:
# python rechainpdb.py mypdbfile1.pdb mypdbfile2.pdb mypdbfile3.pdb
#
# This will generate a new file with all pdbfile (ATOMs and HETATMs) in a single
# file, with e
Paul,
Does your lower resolution structure have the same unit cell as the
model used for MR? If your two crystals are the same except for the
presence of the ligand, then you need to make sure to keep the same
Rfree set for both. Otherwise, some reflections that were previous in
the Rwork
Hi -
I am refining a low (3.7Å) structure with refmac(5.5.0091), and am
having trouble maintaining some secondary structure elements. I would
like to restrain the H-bonding in clear secondary structural
elements, which should help prevent carbonyls in helices from
flipping out, etc, but h
12 matches
Mail list logo
