I can't help but suggest to also try PDB_REDO for tuning refinement.
http://xtal.nki.nl/PDB_REDO/index.jsp
One of the things you get, is exactly what Pavel explains below, how your
structure looks in comparison with others in similar resolution, but also with
the PDB_REDO data bank structures.
Chris,
First, I would try NCS restraints even at ~ 2 A.
Second, any outliers in your diffraction data set that might skew the R values?
Third, have you checked that your refined bulk solvent model is reasonable?
Axel
On Feb 21, 2014, at 6:13 PM, Chris Fage wrote:
> Thanks for the assista
Dear Avinash,
Try DnyDom server for domain motion analysis..
DynDom
http://fizz.cmp.uea.ac.uk/dyndom/
-Best,
Babu
--
www.bm14.eu
On Sat, Feb 22, 2014 at 7:19 AM, avinash singh wrote:
> Dear CCp4b users,
>
> I have a protein which has been crystallized in two different conditions.
> In one
Dear CCp4b users,
I have a protein which has been crystallized in two different conditions.
In one of those conditions, the structure shows the domain shifting.
Is there any programme or online server which calculates the angular shift
in domain when campared to the other condition crystallized st
Hi,
Two things i would like to add:
1) Due to the dependence of A280 on amino acid composition, a simple
two-wavelength 280 and 340 or 320 comparison is not very ideal for
determining the scatter component of the UV absorption of protein/protein
aggregate particles (the usefulness of this sim
Hi Chris,
I personally would go with your "thick" dataset. 90% completeness is
not stellar, but in my opinion not detrimental, either.
I had one project that persistently yielded crystals that diffracted
to rather high resolution (2.3), but in one direction no lunes were
discernible and - cons
Thanks for the assistance, everyone.
For those who suggested XDS: I forgot to mention that I have tried Mosfim,
which is also better than spot fitting than HKL2000. How does XDS compare
to Mosflm in this regard?
I am not refining the high R-factor structure with NCS options. Also, my
unit cell di
Chris,
what you get is not unheard of but clearly you are not in majority: at
around 1.95A resolution distribution of R-factors in PDB is:
Histogram of Rwork for models in PDB at resolution 1.85-2.05 A:
0.093 - 0.118 : 3
0.118 - 0.143 : 75
0.143 - 0.168 : 821
0.
Dear CCP4BB Users,
I recently collected a number of datasets from plate-shaped crystals
that diffracted to 1.9-2.0 angstroms and yielded very nice electron
density maps. There is no major density unaccounted for by the model;
however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
~0.30,
Analogous to Dr. Mirella, we've used the ratio of A320/A280 (for membrane
proteins). In response to a fussy reviewer, I located some relevant references
(refs. 10-13, copied below) when we referred to this in "A high-throughput
differential filtration assay to screen and select detergents
for me
If you need phases, you might change the salt ion(s) to something with
significant anomalous signal, i.e., Rb+, Cs+, Br-, I- instead of Na+ and Cl-.
With such high ion concentrations, you should get some really high-occupancy
sites. In any case it is sometimes handy to have experimental phases i
I want to start off by thanking everyone. The replies, both on- and
off-board, were speedy and numerous. I apologize for the delay in
expressing my gratitude; I was implementing your wonderful suggestions. I
have put together a summary for the archive.
To recap, I was looking for suggestions to
Mark A. White wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> I have a couple of simple awk commands that will calculate both I/sI and
> Redundancy, by
> parsing the the scalepack output log.
> ### I
Eleanor Dodson wrote:
> Jim's point is that SigI is manipluated in the program, and its value
> reflects the
> programmers ideas. If you want to make your hair stand on end process the
> same data with
> SCALEPACK and MOSFLM and get the "Riso" between the 2 SIG estimates! 50% on a
> good day
Phil Evans wrote:
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> Since this seems to be causing endless confusion, here is the
> definition used in Scala for which is what I report to the
> PDB. This is
What about this one?
http://dx.doi.org/10.1107/S0907444912002946
Although the excitation is x-rays and not visible light, you are still
conceivably "identifying protein crystals with visible light". Seems to
mostly come from aromatics. Not sure how much damage you have to do to
get "enough"
Hi Qixu,
Sorry, I don't read this BB very often and missed your message. I assumed the
DEC-1-2003 archives would be online somewhere, but I may be mistaken.
I printed out the discussion and stored it in a notebook. So if nobody here can
point to online archives, I can scan and post the pages on
I am aware of an assay for aggregation (aggregation rate) that is based on
fluorescence measurements. It involves excitation at 280 and emission in the
range 260-400. Is there a reference for the absorbance method?
See
Nominé Y, Ristriani T, Laurent C, Lefèvre JF, Weiss E, Travé G. A strategy
Dear Colleagues,
Applications are now open for BIOCRYS 2014 "Fundamentals of Modern
Methods in Biocrystallography"
organised by Maria Armenia Carrondo and Thomas R. Schneider
*Course sponsored by :* FEBS, BioStruct-X and IUBMB
*
**Date & Location:*20th - 27th September 2014 at the Instituto de
Have you tried lower concentrations of Calcium soaking untli the crystals
do not crack? Or does it crack even at very minute calcium concentration?
On Thu, Feb 20, 2014 at 3:29 AM, Masaki UNNO wrote:
> Dear all
>
> Apologies for the off-topic question:
> We are studying an enzyme that is activat
Dear Prerana,
before starting the crystallization you could try to check the state of you
protein, simply determining the Aggregation Index (AI) from measuring the
absorbance at 280 nm and 340 nm. The AI is then computed using this simple
formula: AI= 100 x (Abs340/(Abs 280 - Abs 340)). Soluble
Hi,
You could change the ratio of paraffin and silicon oil (1:1 or 1:2) and/or use
lower protein concentration.
Best regards,
Vicky G. Tsirkone, MSc
Laboratory for Biocrystallography
Department of Pharmaceutical and Pharmacological Sciences
KU Leuven
O&N II Herestraat 49 - box 822
3000 Leuven |
Hi, Sorry for asking an off-topic question,
I have recently purified a protein having a molecular weight of 40kDa and
concentration of the protein was 8mg/ml. When I tried to set the protein
for crystallisation using micobatch method, the protein started
precipitating in most of the buffer conditi
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Dear Jens,
I recently prepared a cif-file and came across the same question.
With empirical absorption correction ("_exptl_absorpt_correction_type
empirical") the values for T_min and T_max loose a bit of meaning.
Yet, I took the maximal and minimal
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