Dear all,
I have a protein-DNA complex structure at 2 A resolution and I used 3DNA to
calculate the step and base-pair parameters. I am wondering how to estimate
the error for e.g. buckle angle, slide, etc. given the estimated coordinate
error for this data set?
Thank you very much!
Best,
Dear all,
I am refining a structure that has a ligand which contains a thiol group and
forms a disulfide with the cysteine. I created the cif file with the Dundee
server for the ligand and modified the BME-cysteine link cif file to fit my
ligand. I combined these two cif files and feed it to
Dear all,
I was refining complex structures with a DNA oligo that have some
noncanonical bent regions in the middle, the resolutions are fairly good,
around 1.8-2.2A. I used both CNS and Refmac. I found (not surprisingly) that
with Refmac, I got a lot of unusual sugar puckers like C1'-exo that is
Dear all,
I was refining complex structures with a DNA oligo that have some
noncanonical bent regions in the middle, the resolutions are fairly good,
around 1.8-2.2A. I used both CNS and Refmac. I found (not surprisingly) that
with Refmac, I got a lot of unusual sugar puckers like C1'-exo that is
Dear all,
Sorry this might be another naive, non-ccp4 question~
I was trying to make a composite omit map with CNS, but during torsion angle
dynamics, it always reports an argument out of range error like the
following:
-- step= 5 at 0.02000 ps
Hi all,
I have always been wondering... for a data set diffracting to say
2.15Angstrom but in the highest resolution shell (
2.25-2.15) the completeness is 74%, should I use merge all the data and call
it a 2.15 A dataset or I should cut the data set to say 2.25 A where the
highest resolution
. Redundancy
3. I / Sigma
4. R merge statistics
Not just one of them. If you are pushing it too far, you will see the
effect in later refinement step..
With 74% completeness, how does the other parameters look like?
HTH, Partha
On Mon, Mar 17, 2008 at 10:06 AM, Melody Lin [EMAIL PROTECTED] wrote
Dear all,
Thank you very much for the useful suggestions! I definitely learned a lot
from these discussions. Now looking back at my datasets, I think the
incompleteness likely results from high mosaicity (1.009) and anisotropy of
the crystal. Detector is square, but the distance is short enough
Dear all,
sorry for the off-topic and possibly very naive question- but does anyone
know what happens if normal protein is put in detergent-containing aqueous
solution? how much detergent can a regular protein tolerate? I was trying to
search literature but couldn't find any...
Thank you greatly
