In the Southern realms of the US at least, academic centers maintain room temperature at WSRT year round because “77°, ew gross.” In fact, the only time those air conditioners turn off is when we are struck by errant polar vertices and our power grids fail. Postdocs described the experience as
I started a ccp4 thread a few years ago about RSRZ score calculations
favoring trimmed side chains because they produce better scores. Based on
what I could find at that time, it looked like the density of your
structure was compared to the density of that residue type in submitted
PDBs of similar
I think the typical Akta configuration has the prefilter installed after
the mixing pump, but before the sample loop. That is where it is on mine at
least. It wouldn't stop sample precipitate from loading on the column.
Technically, it would probably still work if you installed the prefilter
after
Hi Bing,
This is the result of the new PDB deposition system being buggy. I had a
similar problem with imidazole recently. This is the solution given to me
by the PDB annotators.
Please choose from the instance page:
type of ligand: heterogen,
then give alternate ligand ID as IMD, (in your
Hi all,
I am trying to figure out the best way of reporting changes in dimer
orientations between three structures. I have an apo, a drug-bound, and a
homolog dimer structure. I had originally decided to calculate the angle
from the rotation matrix generated by LSQKAB, but the translational
Hi all,
I've been playing with the new PDB validation service. It is very pretty
and kudos to all the hard work that has clearly gone into it. I did notice
however that the way the information is presented, there seems to be a bias
towards truncating side chains versus modeling them with higher
Hi all,
My google-fu has failed me once again so I am turning to the collective
knowledge of the bb. I'm working on a blobology challenge at the moment and
have hit a wall. Is anyone aware of an ion that coordinates to lysine and
prefers octahedral geometry. The mystery ion seems to have perfect
Hi all,
I have two nice, but a hair under-complete data sets that I am trying to
merge together. If I run aimless on them separately everything looks
beautiful. When I merge them together the CC1/2 is still good but all the
various and sundry Rs sky rocket. When I go to the log file and look at
responses.
Katherine
On Thu, May 8, 2014 at 12:18 PM, Craig Bingman cbing...@biochem.wisc.eduwrote:
How close are the cell constants?
On May 8, 2014, at 12:17 PM, Katherine Sippel katherine.sip...@gmail.com
wrote:
I forgot to mention the space group is P1. Sorry about that.
Thanks,
Katherine
]
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Katherine Sippel [katherine.sip...@gmail.com]
Sent: Tuesday, February 18, 2014 12:08 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] High Salt Cryo
Hi all,
I'm looking for a cryo condition for high NaCl (3+ M
Hi all,
I'm looking for a cryo condition for high NaCl (3+ M) crystallization
condition. I would do it the proper way, but our beam/cryostream is down.
I've tried a bunch of things at the moment. Ethylene glycol and PEG 400
nuke the crystals immediately even at low concentrations. Prolonged
To answer Mark's question, if your crystals are capillary mounted then
planes are no problem. My protocol is to mount them, wrap them in cotton
batting, put them in a 50 ml falcon tube, and pack that in bubble wrap. I
managed to get them through security in my carry-on with no issues. I
suggest
Alternatively you could make a stock solution of citric acid (say 1 M for
example) and stock solution of sodium citrate (also 1 M). Mix them in the
appropriate ratio to ballpark the right pH and just adjust up or down with
the stock solution. The concentration of citrate will be the same no matter
Hi all,
I thought the bulletin board might be interested to know that one of the
contributors on Popular Science is featuring a webcomic series on X-ray
crystallography. The first post went up yesterday and can be found here (
http://www.popsci.com/blog-network/boxplot/x-tallographers ). If
Hi Acoot,
There are a lot of great suggestions here already. I've also run into this
phenomenon in couple of cases. The first was a binding protein in mixed
bound and unbound forms. The second was a case of heterogeneous
post-translational modification. In both cases I could only get crystals
Hi all,
I was wondering if anyone knew of a software or server to mine the PDB for
a specific class of interactions? I've tried PDBeMotif without much luck
and I thought I'd check to see if there was an alternative before I go
re-inventing the wheel.
Cheers,
Katherine
--
Nil illegitimo
Denizens of the bulletin board,
I would like to tap into your vast knowledge of all things protein
expression. Is anyone aware of a cell line or even a
transformable/transfectable construct that produces high processivity
ribosomes. I.E. one that can translate to the end of difficult mRNA without
I forgot to mention that in this case gene optimization and eukaryotic
expression don't help. It's a product of the protein sequence itself.
On Tue, Sep 24, 2013 at 10:29 AM, Katherine Sippel
katherine.sip...@gmail.com wrote:
Denizens of the bulletin board,
I would like to tap into your
Thermo Scientific/Pierce has gotten into the protein purification game
recently. The resin is slightly cheaper (USD $975/100 ml versus $1656 for
GE) and the binding capacity is equivalent. I haven't rigorously run any
regeneration tests though. Our local sales rep actually sent us a 1 ml spin
I'm not sure that a library of ligand electron density would be an entirely
good thing. I guess something small like an acetate or DMSO would be
relatively consistent but larger things like PEGS or even glycerols are
going to be dependent on the nature of the binding site. A good example
would be
On Tue, Mar 19, 2013 at 9:34 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
One might argue that since basically all organisms share the convention
(are there exceptions, even?), that it must be the best of all possible
conventions.
There are actually lots of exceptions. For example
Hi all,
I was wondering if anyone out there has any anecdotal evidence of intein
tag cleavage buffer compatibilities outside those suggested in the IMPACT
manual (pH between 8 and 9, 0.1-2M NaCl or 0.1% Triton X-100). Specifically
I'm looking for whether I can reduce the pH to 8, acceptable
You know if you took a dremel to an insulated benchtop cold box to make USB
shaped holes, lined the bottom with a layer of desiccant, and used a little
vacuum grease to seal it up you might actually have a workable, long term,
freezer storage system.
Wow, the things you think up when you're
As a follow up to Roger's statement if you are doing any sort of analytical
metal analysis be careful with the controls (metal-free water/acid washed
glassware). Also most AC/heating systems include galvanized steel in the
duct work that spits out Zn like crazy and can screw up your measurements.
-purification.
Thanks for all your help,
Katherine
On Mon, Sep 24, 2012 at 9:38 AM, Katherine Sippel
katherine.sip...@gmail.com wrote:
Hi All,
I've recently swapped over to expression in the ArcticExpress(DE3) cells
for a particularly rock-like protein. I've got soluble expression but I'm
having
Hi All,
I've recently swapped over to expression in the ArcticExpress(DE3) cells
for a particularly rock-like protein. I've got soluble expression but I'm
having the issue of Cpn60 (the overexpressed chaperonin) piggybacking along
with the tagged protein. Google-fu and the CCP4bb archives
The 3tvn coordinates/SF were released today. I'm not sure what the lag time
is between the PDB and EDS but you'd probably need to download the
structure factors and generate the map yourself.
If you're not in a super rush I know the person who refined that specific
PDB and I may be able to get
From personal and recent experience I've solved a structure using only
iodine anomalous at Cu K-alpha from a RT crystal (a capillary mounted one
at that). The anomalous signal from iodine is surprisingly robust on a home
source even at room temp.
Katherine
As an aside for those who feel that
It would be helpful if I finished my own sentences. As an aside for those
who feel that capillary mounting is a lost art among the newer generation I
assure you it isn't. All you need is a busted cryo system and a crystal
backlog to get past the intimidation factor.
Katherine
On Wed, Jun 6, 2012
Hi Ed,
I've actually run that exact test in phenix as an exercise to prove to my
PI the validity of occupancy refinement. Though as a disclaimer it was a
1.2 angstrom data set and this was an alternate conformation situation. I
ran different input occupancies without occupancy refinement and
That is probably because you pH Tris with HCl rather than HEPES with NaOH.
The Ksp for Zn(OH)2 is 3x10^17 so the excess hydroxides are probably what
are killing your solution.
Cheers,
Katherine
On Fri, May 11, 2012 at 11:43 AM, Rajesh Kumar ccp4...@hotmail.com wrote:
If there is no cure ,
Keller
j-kell...@fsm.northwestern.edu wrote:
Just to make sure I understand pH correctly: isn't it true that the [OH-]
should always be the same at a given pH (by definition)?
JPK
On Fri, May 11, 2012 at 11:48 AM, Katherine Sippel
katherine.sip...@gmail.com wrote:
That is probably because
On Wed, Apr 4, 2012 at 10:31 AM, Roger Rowlett rrowl...@colgate.edu wrote:
I have also seen a recent paper where radiation damage of a bound protein
ligand was apparently observed in a synchrotron beam.
That was a manuscript were I would have happily given the coordinates and
structure
Might I suggest looking to Sean Seaver and the P212121.com as an example of
a a successful crystallographer science blogger though the site has shifted
more towards a consumable supplier in recent years.
I would also consider looking into adding an RSS feed to your site so that
those people
I agree with Herman about personal preference but it also boils to our job
as crystallographers to educate non-structural end-users. The fact of the
matter is that a lot of researchers use structures without looking at the
nuances of the PDB. It's actually pretty common among biologists to
Well if you think about it technically God produced plants within three
days which if far too little work for a thesis. Maybe it could count as
preliminary results for one aim of a thesis proposal so it might be enough
to get PhD candidacy depending on how demanding your committee is. You
could
Might I suggest consulting the CCP4 user community wiki on the topic:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Improving_crystal_quality
Good luck,
Katherine
On Thu, Jan 26, 2012 at 9:33 AM, Theresa H. Hsu theresah...@live.comwrote:
Dear crystallographers
I have a
Hi Rashmi,
In my experience native (even blue native) on proteins around that pI is
sketchy at best. The electrophoretic mobility once it gets past the
stacking gel goes to crap meaning long electrophoresis times and it needs
to be done on a chillable system or in a cold room. If this is a
Hi all,
I've run into a bit of a protein purification conundrum and wondered if
anyone had encountered a similar situation. I've exercised all of my
google-fu and can't find anything. It's a fairly straightforward setup;
His-tagged protein and Talon Co2+ resin, load lysate, wash with 5 mM
In a non-computational capacity would also suggest perhaps resequencing
your clone. Occasionally the published sequences are off, the specific base
is polymorphous or there is also the possibility that you introduced a
mutation somewhere. That would be the cheap and easy way to definitively
answer
For drawing a 2D fold topology I'd suggest TopDraw (
http://www.ccp4.ac.uk/html/topdraw.html). To see if you structure looks
like other structures I'd look at the DALI server (
http://ekhidna.biocenter.helsinki.fi/dali_server/). Dali is pretty good for
digging out results/discussion fodder because
this job. Again, thanks.
Cheers,
Katherine
2011/11/1 Katherine Sippel katherine.sip...@gmail.com
Hi Andreas,
It is much larger and looks slightly less like Chthulu cut himself shaving
(I'm going to crystallographer hell for that comment). For those interested
I've put the picture on Photobucket
Hi all,
I'm going to interject into the middle of this rousing though protracted
debate to pick your brains. I am in possession of a rather large and intact
brass scale Kendrew model (sans mirrors). Due to facility restructuring we
no longer have room for it. I have approached the local health
On 01/11/2011 2:34, Katherine Sippel wrote:
Hi all,
I'm going to interject into the middle of this rousing though protracted
debate to pick your brains. I am in possession of a rather large and
intact brass scale Kendrew model (sans mirrors). Due to facility
restructuring we no longer have
] Manuscript in progress
Katherine Sippel, PhD
Postdoctoral Associate
Baylor College of Medicine
-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710*
**
**
*
*
--
*From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Katherine
Sippel [katherine.sip...@gmail.com]
*Sent:* Friday, October 28, 2011 8:06 AM
*To:* CCP4BB
I have said my piece of the issue of depositing but there is one comment I
would like to address.
Besides, I thought that by now there are some standards on how data should
be processed (this has been discussed on this BB once every few months, if
I'm not mistaken). Isn't that part of the
Hi all,
I was wondering with the all of the advances in microbeam technology and
hardware, what is the best methods for cryoprotecting microcrystals? Are
oils better than solutions? How do you address the excess liquid issues? Is
there a way to test the conditions prior to shipping it off to the
Ha. That is obviously it. I failed to account for Brownian motion in the pdb
file itself. Properly modeling this is really going to mess with my data to
parameter ratio.
Katherine
On Tue, Jul 12, 2011 at 12:54 AM, James Stroud xtald...@gmail.com wrote:
On Jul 8, 2011, at 11:13 AM, Katherine
Hi all,
I am putting the finishing touches on a structure and as a good little
crystallographer I am running it through Molprobity and PDB validation to
make sure everything clears before deposition. Everything was looking
alright until I threw the file into the PDB validation server and suddenly
Hi again,
I have an update. The nice people at the PDB have gotten in touch and they
think it might be a bug. They are looking into it.
Thank you for all the off-board replies and I hope you all have a wonderful
weekend.
Katherine
On Fri, Jul 8, 2011 at 1:13 PM, Katherine Sippel katherine.sip
found this to
be the case with 1M concentrations of citrate and acetate as well. Unless
there is a specific binding site to organize the molecule in regards to
the protein it just loiters in the solvent that you are flattening anyways.
Just my two cents,
Katherine
---
Katherine Sippel
Hi all,
I recently upgraded (if you can call it that) to Ubuntu 10.10 and I'm having
some issues with CCP4 and file recognition. I suspect this is an Ubuntu
issue rather than a CCP4 issue but I'm hoping someone will have an idea. I
downloaded the CCP4-Lin-generic.tar and ran the install.sh. It
Bingo! I might suggest adding this library to the list of packages to
install in the platform specific portion of the problems page documentation.
Thanks again.
Katherine
On Fri, Mar 11, 2011 at 4:01 PM, Ben Eisenbraun b...@hkl.hms.harvard.eduwrote:
Hi Katherine,
terminal and there are no
thank you all for the quick responses.
Katherine
On Wed, Feb 23, 2011 at 10:51 AM, Katherine Sippel
katherine.sip...@gmail.com wrote:
Hi all,
I have sort of an oddball question regarding how PISA reads the ligand file
into the program for calculations. Does the element symbol of the PDB file
Hi all,
I have sort of an oddball question regarding how PISA reads the ligand file
into the program for calculations. Does the element symbol of the PDB file
take precedence over the atom name or residue name?
Specifically, if a ligand contains either atom names or residue names that
are
Hi all,
I was wondering if you know of a program that can do protein sequence
alignments around experimentally determined equivalent residues (i.e.
biochemists have determined via mutagenesis and kinetics that residues 3,6
and 9 of protein X are the equivalent of residues 7, 14, 21 in homologous
In our hands the Rsymm difference after scaling was 3% and the crystals were
not particularly isomorphous (1.2 degree difference in beta angle). We were
also shooting at room temp and still found a solution. We were using an in
house source to optimize the anomalous signal, so if the data was shot
Hi Debajyoti,
For my low pH phasing (pH 3) the thing that worked for me was the Magic
Triangle. It works best at Cu K alpha (i.e. home source). There is a Mad
Triangle that works at synchrotron sources as well. You can get it all made
up from Hampton or Jena Biosciences but you can also buy the
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