Hi Kavya,
Which validation program did you use? How big is the deviation (in sigma
values)? Is it the only outlier? What is your overall bond angle rmsZ?
Using external restraints is a bit over the top here, especially if it is the
only outlier. If your rmsZ is high (close to or over 1) then
Sir,
I used RCSB validation server. Deviations are as given below -
Deviation Resi AT1 - AT2 - AT3BondDict Std
Angle ValueDev
--
3.2ARG NE - CZ - NH1
Dear Kavya,
I would examine the electron density of your Arginine. It may be present in two
alternative conformations and you may have fitted the Arginine in the middle,
e.g. with the NH1 in one conformation and the NH2 in the other.
The Arginine may also just be incorrectly fitted. Using
Dear Kavya,
First try Herman's suggestions. You can try changing the restraint weight but
it will probably not solve the problem; it may hide it. If you cannot solve the
problem and you did the best you can do, you can deposit the model with the
outlier. The PDB does not reject models with
Dear ccp4
I have been performing trials on a protein DNA complex for a while now and have
not seen any crystals form. Today I checked an old plate (over a month old) and
I see 4 large crystals. *excitement* Three of them look tetragonal in shape
(like a pyramid) and one of them looks
Dear Careina,
I would be cautious of using dyes. Much better to 1) try in-situ
diffraction if possible as this is least invasive or 2) pick a sensible
cryo and just freeze the crystal(s). I would try to same something from
the experiment for seed stock possibly sequencing.
Dave
David
What else in in the conditions? Calcium Sulphate/Phosphate is poorly soluble,
so if there is any sulphate or phosphate in your condition I would be
suspicious.
The age of the plate is also a bad sign, as evaporation over an extended time
can lead to salt crystals. Check the well solution for
Sir,
Thank you Sir. It worked. I used alternate conformations
which differ by 180 deg around CZ-NE bond. Now there is no
angle deviation error.
Thank you all for useful suggestions.
With Regards
Kavya
what you may have is two alternate conformations - i.e. your current one
and one with the
P.S.: The C5 is what we had in Bochum. Also not perfect, but I guess theres
no perfect machine ..
Von: Clemens Steegborn [mailto:clemens.steegb...@ruhr-uni-bochum.de]
Gesendet: Donnerstag, 28. März 2013 13:58
An: 'Clemens Steegborn'; 'CCP4BB@JISCMAIL.AC.UK'
Betreff: AW: [ccp4bb] cell
Dear Careina,
altough your crystals does't take up the Izit dye it sounds promising. The
uptake of Izit depends on the solvent channels of the protein molecule -
sometimes the dye just can't enter the molecule.
Concerning the Calciumchloride - if the concentration is not too high and
without
Hi Folks,
Does anyone know of an accurate way to mine the PDB for what percent of
total X-ray structures deposited as on date were done using molecular
replacement? I got hold of a pie chart for the same from my Google search
for 2006 but I'd like to get hold of the most current statistics, if
Post-Doctoral Fellow (m/f) for the Macromolecular Crystallography
/in-crystallo/ spectroscopy facility : Grenoble, France
You will play a major role in the operation and development of the ESRF
/in-crystallo/ spectroscopy Facility (ID29S) dedicated to the
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Dear Raji,
the numbers you have accumulated might already be accurate, it is more
a question of how precise your numbers should be - and this might
become a long discussion without resulting in a single answer:
Take into account that the PDB query
Structures of a protein-ligand complex are often determined without the need of
running a molecular replacement program: a difference Fourier is generated to
locate the ligand, usually after a few rounds of rigid bodies and / or atom
positional refinement..
They may account for many of the
From my own db program:
Number of entries in histogram: 711
Total number of instances : 78467
0 48249 0.6149 MOLECULAR REPLACEMENT
1 8557 0.1091 NULL
2 5632 0.0718 SAD
3 5128 0.0654 MAD
4 3600 0.0459 FOURIER SYNTHESIS
5 1762 0.0225 OTHER
6 1171 0.0149 MIR
7
Thanks to everyone who responded. I appreciate your pointing out the
caveats of such statistics mining expeditions.
I remember (with no accuracy or precision) sitting in a lecture by Wayne
Hendrickson years ago and watching him cringe at the notion of considering
the simple case of difference
Just to round up this topic, a bug report was submitted to PDBe concerning
entry 2wlv and the PDB has how responded acknowledging the problem. An updated
entry will be available in one week.
As pointed out by Savvas, it is very likely the CRYST1 record was manually
edited prior to deposition
On 15 Apr 2013, at 17:19, Michel Fodje michel.fo...@lightsource.ca wrote:
I imagine somebody accidentally deleted a space between P 21 21 2 and 18 and
tried to fix it by adding it back, between 1 and 8.
As this has now been mentioned twice in this discussion it should probably be
noted
I may be biased, but the only way to really be sure is to shoot them.
If you see no spots at all, be sure to do a wide oscillation (rotation
during the exposure) shot as well. It is not unlikely for a salt
crystal to be oriented so that no relps are on the Ewald sphere, giving
no spots.
Protein-DNA complex crystal with channels too small for the dye is *extremely*
unlikely, imho.
Original message
From: Ulrike Demmer ulrike.dem...@biophys.mpg.de
Date: 04/15/2013 8:48 AM (GMT-05:00)
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] salt or not?
Dear
On Mon, 15 Apr 2013, Raji Edayathumangalam wrote:
Hi Folks,
Does anyone know of an accurate way to mine the PDB for what percent of total
X-ray structures deposited as on date were done using molecular replacement? I
got hold of a pie chart for the same from my Google search for 2006 but I'd
The only way to really do creative stats on the PDB is to just
download the whole thing. It is a sobering thought to realize just how
tiny it is! Less than 17 GB. Once you've got it all on your hard disk
you can start writing little programs to look for different things. I
have posted
On Mon, Apr 15, 2013 at 11:47 AM, James Holton jmhol...@lbl.gov wrote:
However, I'm sure the day is not far off when phenix.refine or the like
will check if the starting R factor is too high and just automatically
invoke a run of MR to see if something clicks.
I think the latest Phaser code
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