Actually, with a non-origin peak height only 1/4 of the origin and a
translation that does not correspond exactly to a centering operator, Phaser
has a very good chance of coping with this case. I think that the space group
ambiguity of whether the 2-fold parallel to x is a screw axis or a
Hello,
Can anyone let me know how to calculate solubilisation and refolding
efficiency. We perform solubilisation and then refolding and check by HPLC
if refolding is completed or not [single peak on HPLC]. how do i determine %
efficiency of refolding. kindly guide me.
regards,
megha
Well, I've actually had success using phaser for placing 6 monomers in the a.u.
P41212 space group BUT only after the first monomer was fully built into the
initial map (pdb entry 2pan), in other words when the probe was 100% identical
in sequence and structurally close enough to the target.
James
All great stuff.
Ø The individual crystals were not twinned (or at least I would be VERY
surprised if they were)
Can this be tested? The spots should show fringes around them corresponding to
the shape transform of the nano-crystal. If twinned, the intensities of the
fringes
How:
1. measure total protein before refolding (eg by absorbance at 280)
2. Purify refolded fraction by gel filtration in FPLC
3. measure total protein after refolding
4. calculate efficiency ...
Why?
I don't see the reason to know the efficiency. If after refolding I
would get enough in a
Are you sure these are real FP=0 or reflections which werent measured
but have been added for completeness of the h k l list.
The check is whether the SigF is also 0.00 - in that case they are
genuinely missing..
Eleanor
On 02/09/2011 11:34 PM, Ed Pozharski wrote:
I observe under some
Hello,
I received two private emails answering my question. Both pointed out that the
residues are allowed to go beyond the actual residue numbers in the PDB file, so
that specifying e.g. residues 1 through works just like a wildcard.
Cheers, Tim
On Wed, Feb 09, 2011 at 12:26:34PM +0100,
Anyway, I thought that was a cool idea, but like so many other cool
things, it had to be cut from the Nature paper. Admittedly, the
problem has not actually been solved yet. This is why we used
REFMAC in TWIN mode.
Is that a hint on the:
a. wisdom of the editor
b. wisdom of 'the third
Excellent point and no, these are not missing reflections. SigF is not
zero. Also, if I am not mistaken, missing reflections in the MTZ format
are recorded as NaN.
Ed.
On Thu, 2011-02-10 at 12:17 +, Eleanor Dodson wrote:
Are you sure these are real FP=0 or reflections which werent
This does sound like a bug. If one of h,k,l are zero then the reflection is
centric in P222 so the truncation will be different
I just ran a test on an orthorhombic dataset (P212121) of mine and I do indeed
see some strange F=0, sigF0 reflections, but in Charles Ballard's
development version
Would it be true that the anomalous differences could not be measured
in these types of datasets, because one would not know which
Friedel/Bivoet reflection one is measuring in a given frame? Perhaps,
given anomalous signal, there would be a way to tease out which
orientation one was looking at
Dear Kendall
2011/2/10 Kendall Nettles knett...@scripps.edu:
When I real space refine my ligand the hydrogens fly away. The ligand pdb
file and cif file were generated with progdr. I'm using Coot 0.6.2-pre-1.
Kendall
This could be a problem with the naming conventions of pdb versions. I
That happens also for me with all hydrogens, regardless if they belongs to a
ligand or protein.
Best solution for me is stripping all hydrogens out of the pdb. Manipulating
the file in coot and readding them and start of the renfinement.
Christian
Am Donnerstag 10 Februar 2011 17:04:18
===
SYNCHROTRON BEAM TIME FOR MACROMOLECULAR CRYSTALLOGRAPHY AT SLS
===
Proposal application deadline: Tuesday, February 15, 2011
Periods:
May 1, 2011 - August
I hope everyone understands that I am not the corresponding author on
this paper! That is Henry Chapman. He, and most of the other authors
have been slaving away on this problem for most of their professional
careers. To be honest, I never did think it was going to work, and I
was
Our main reason for thinking that the nanocrystals were not twinned is
because the regular crystals of the same form, grown under very
similar conditions were not twinned (1jb0). The space group, unit cell,
and indeed the structure in the ASU were all the same. In fact, I don't
think
Dear all,
Twin refinement has yielded Rwork/Rfree values of about 0.10/0.12
for a nice quality 1.8A dataset (Rmerge 6%, space group I4, twin fractions
0.6/04) and almost the same R/Rfree (0.095/0.115) for another 1.5A nice
quality data set (Rmerge 6%, space group I4, twin fractions
Dear all:
A postdoctoral position is available in the Mitra Lab at the School of
Biological Sciences at University of Auckland to investigate 3-dimensional
structure/function of two membrane proteins involved in cation and solute
transport using primarily X-ray crystallography, but also
Dear CCP4 users,
I am trying to use FSEARCH to position a SAXS envelop in an attempt to solve
a molecular replacement case.
Could you explain what the x,y,z values in the output stand for. Do they
represent the position of the center of mass of the molecule in the unit
cell ?
I would be
Thanks, Garib
It might be the case.
As a matter of fact, you are welcome to look at the original data here
http://www.rcsb.org/pdb/explore/explore.do?structureId=2GL5
The data turned out to be twinned ( I also have other datasets - all
with certain degree of twinning) and now I am trying to
Just a warning: When doing twin refinement (and in general) you should always
use original data for refinement. After refinement data may be different (in
case of twin de-twinned).
I will have a look as soon as I have some time.
regards
Garib
On 10 Feb 2011, at 22:06, Patskovsky Yury wrote:
Hi Yury,
- make sure you correctly generated free-R flags, so there is no cross-talk
between test/work sets. Illustration: see page number 123 here:
http://cci.lbl.gov/~afonine/for_ccp4/PavelAfonine_PHENIX.pdf
- compare regular vs missing-fobs-filled maps. See pages188-190 here:
Dear Yury
I looked at this data and such drop of R/Rfree when you switch from non-twin to
twin in the presence of twinning is expected.
When you said that electron density is too good I was afraid that there is
strong bias. But at least for the case from the pdb (2gl5) you can see a lot of
Dear colleagues,
I would like to draw your attention to an upcoming webinar to be presented by
Brian Matthews, Ph.D. titled Protein Crystallography: Getting in on the Ground
Floor. Brian Matthews received both his B.S. (1959) and Ph.D. (1964) from the
University of Adelaide, completing his
Hi Yuri,
The biggest drop I've seen as the result of detwinning is 10% lower R-free.
Perhaps the detwinning has helped your refinement in othed ways. What R(-free)
do you get when you take you pdb from the twinned refinement and your input mtz
file and do 0 cycles of refinememt without
Hi Yuri,
The biggest drop I've seen as the result of detwinning is 10% lower R-free.
Perhaps the detwinning has helped your refinement in othed ways. What R(-free)
do you get when you take you pdb from the twinned refinement and your input mtz
file and do 0 cycles of refinememt without
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