It may be time for our annual I/sigmaI discussion.
Please note that is what the RCSB expects from you and it is
generally lower than /. Some packages do not output
in an obvious place for you to put in your Table 1. :)
On Wed, 6 Oct 2010, Ed Pozharski wrote:
You don't need twinning to
This cryocrystallography webinar lists some common cryoprotectants:
http://www.rigaku.com/protein/webinar-001.html
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Chris
Weichenberger
Sent: Thursday, September 09, 2010 7:34 PM
To: CCP4BB@JISCMAIL.A
Have you tried to use glycerol or ethylene glycol as the precipitant? What
happens when you go to 50% or higher concentrations?
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Roger
Rowlett
Sent: Wednesday, August 25, 2010 9:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject
It might be instructive to draw a precession-like diagram of your
reflections in reciprocal space. Remember that reciprocal space dimensions
are generally in reciprocal Angstrom and volumes raise those dimensions to
the third power. Thus (1/12)^3 to (1/15)^3 is not a big volume.
How many reflect
d*TREK will process compressed images with the following extensions: .gz
.bz2 .Z .pck and .cbf
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian
Tickle
Sent: Thursday, May 06, 2010 6:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Processing c
I thought some of you would enjoy a little conditional probability
discussion found in the NY Times today, since this is a big part of
crystallography nowadays. I'm always on the lookout for good ways to teach
Bayes's theorem.
http://opinionator.blogs.nytimes.com/2010/04/25/chances-are/
Jim
I would test several hypotheses. You have a multitude of salts to choose
from. Test them all.
Let me ask you this: What anions can you test? What's already on your
shelf of chemicals? What did you test already?
Jim
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Beha
Yeah, but how was I/sdI determined? Most programs allow you to multiply
your sdI by any number you want which in turns means that you can create
any I/sdI that you want.
A multiplicity of 11 does not explain a high Rsym to me.
Jim
On Thu, 22 Apr 2010, Frank von Delft wrote:
Yeah, stop worr
One might also check the pH of your crystal and the number of hydrogen bond
donors from the putative sulfate (zero?) or the putative phosphate
(non-zero).
I'm alluding to the structures of the sulfate-binding protein and the
phosphate-binding protein from Quiocho's group.
Jim
_
From: CC
In the instance where we grew crystals is isopropanol, we found they also
grew in PEG6000. The best crystals grew in isopropanol, so we just
harvested the crystals into a similar PEG6000 solution. I would imagine
that you can get the crystals to grow in something beside isopropanol
especially now
The weighted mean is used. Wikipedia
http://en.wikipedia.org/wiki/Weighted_mean has the equation(s).
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Eleanor Dodson
Sent: Thursday, March 18, 2010 4:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp
20 g/L is the same as 20 mg/ml, isn't it? That does not seem particularly
high to me.
Why not try 200 g/L?
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jan
Rash
Sent: Friday, March 05, 2010 8:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] crystallization o
If you look at the structure of glycerol and how it binds to your protein,
what other compounds are similar yet probably won't bind? You essentially
are trying to unoptimize substrate binding which is probably easier than
optimizing substrate binding.
It seems to me that possibilities are anythi
Rigaku has a couple of Webinars on cryocrystallography that you may wish to
view:
http://www.rigaku.com/protein/webinars.html
Jim
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Claudia Scotti
Sent: Thursday, February 04, 2010 3:55 AM
To: CCP4BB@JISCMAIL.AC.UK
S
I do not know the effect myself, but the idea of "vibration fee" has been
tossed around a while. I believe that no vibration reduces the amount of
nucleation that one might get, thus a vibration-free environment is
detrimental when screening for hits. If you already have a method to grow
crystals
g decreases more rapidly with increasing detector-to-sample
> distance than Bragg reflections. For example, Jim Pflugrath, in his
> 1999 paper (Acta Cryst 1999 D55 1718-1725) says "Since the X-ray
> background falls off as the square of the distance, the expectation is
> that a
2.29 Angstrom is an excellent wavelength for Cl, Ca and S anomalous
scatterers. This is the wavelength produced by a Cr home source.
Some older references:
Acta Crystallogr D Biol Crystallogr. 2003 Nov;59(Pt 11):1943-57. Epub 2003
Oct 23. Away from the edge: SAD phasing from the sulfur anomalous
A JPEG has fixed colors for the pixel values. A diffraction image has to
use a viewer to convert the pixel values (counts) to a color.
One problem with just using a converter to jpeg is how to convert
intensities to color (i.e. computer display values).
A demo version of d*TREK is freely availabl
Have you tried to grow the crystals in the presence of small amounts of
cryoprotectants?
For example, use sucrose, glycerol, ethylene glycol, trehalose, glucose,
sorbitol, various salts in the crystal growth.
One can use concentrations of the additives in the 1% to 4% (w/v or v/v)
range. The
Have you tried to grow the crystals in ethylene glycol or glycerol instead
of isopropanol?
On Mon, 6 Jul 2009, kumar wrote:
Dear members,
I have protein crystals grown in a condition with Isopropanol (13%) and
citric acid (0.2 M). When I transfer the crystals to cryo-buffer (30%
glycerol or 2
I have a protein-DNA complex grown in 30 -40% MPD/0.2M Ammonium
sulfate/5% PEG 400/ 0.1M Tris (8.5).
...
I tried to grow crystal without AMSO4 or 0.1M AmSO4, but no crystals was
shown up.
So how would you test the following four hypotheses?
1. Sulfate is not required, ammonium is.
2. Ammoni
The cryoprotectant is 1,6 hexanediol.
Jim
On Thu, 2 Apr 2009, HanJie_Heng Chiat Tai wrote:
Hi,
I have a crystal grown in 2.1M 1,6 hexanediol/0.1 M tro-sodium citrate (pH 6.5).
What's the cryoprotectant can be used to flash cool this crystal?
Any online protein crystal cryoprotectant
That leaves the question of how to label these statistics in a consistent,
clear and concise way: suggestions?
Phil Evans
Here is a suggestion. :)
FWIW, dtscaleaverage labels the mean I/sigmaI of the individual input
reflections as "I/sig unavg". That is, before any averaging is
performed
If I understand you correctly, you are writing about sucking a crystal up
into a small capillary. This is an ancient technique used with the very
first protein crystal diffraction data collection in the 1950s and 1960s
that is still used today. You can use a small 1 ml plastic syringe for the
pos
Hi Tassos,
It's a bit early in the year to have our annual I/sigI discussion on the
CCP4BB, isn't it?
Usually, we wait until at least April 1. :-)
>.
>d*TREK could confuse people further as to which one should be used for
reporting and >decision making.
>
>.
>The Big Question Again:
On Mon, 23 Mar 2009, Phil Evans wrote:
I'm happy to change the column titles if it makes it clearer. Actually the
"I/sigma" column in the Scala output is not very useful:
it is / RMSscatter, ie the mean intensity/mean error, for individual
observations, not taking into account multiple measur
Well, what do you expect the anomalous signal contributed from your 45
seleniums in a perfect world to be when the asymmetric unit contains 1300
aa? Do you think a dataset with Rmerge of ~15% is good enough to detect a
signal of even 2%? (Note: I did not do the calculation, so I just made up
Put a small piece of dry ice on the opposite side of the plastic from the
crystal. Perhaps the difference in thermal expansive coefficient will let
the crystal(s) break away. Don't overdo it though. This is a trick that
Gary Gilliland taught me.
Jim
On Wed, 28 Jan 2009, Savvas Savvides wro
I wonder if the early use of the shortened "structure amplitude" is
because it was a pain to do any typing, word processing, typesetting, etc
before Gutenberg.
But soon crystallographers will be solving all their structures on their
cell phones and also just text messaging manuscripts to edito
Ian, are you saying that one might need to know some crystallographic
theory in order to determine space groups? Or can we simply click a few
buttons in a graphical user interface and be done with it?
Jim
On Mon, 15 Dec 2008, Ian Tickle wrote:
But that only means that the SF contribution f
A good cover -- judiciously used -- goes a very long way in reducing ice
in dewars whether the dewar is made of foam, glass or stainless steel.
If you keep your dewar covered with a lid that extends on the outside of
the dewar down a few centimeters below the dewar edge, you will have
minimal
There is ALWAYS anomalous scattering. You do not have be at the
absorption edge to get it. The question is just whether your experiment
is good enough to detect it.
So your question of "overlapping" always has the answer Yes, but I would
remove the words "absorption edge" from your question.
How would you tell the difference between a unit cell shift and a wavelength
shift when collecting diffraction data at a synchrotron beamline? Well, all
the cell length would scale by the wavelength, so that would be one hint
that the wavelength changed. If a got longer and c got shorter, then it
I've been in that cold room / hutch. I never heard of it being flushed
with LN2. I think that is just to make the room sound cooler.
Jim
On Thu, 19 Jun 2008, Mischa Machius wrote:
Sadly, I have never seen the room being used. Perhaps one of the 'older'
Martinsrieder on the forum has seen it
Whatever dye(s) you use, be sure to run some positive and negative
controls to see how the dye really works.
Jim
On Sat, 14 Jun 2008, Mark Del Campo wrote:
Before I place an order for some Izit, are there some other dyes I can
use to check if I've got a protein crystal?
Thanks,
Mark
Folks, sorry for the belated announcement, but I noticed the application
deadline is creeping up on us. Jim
X-ray Methods in Structural Biology
Cold Spring Harbor Laboratory
October 13th-28th, 2008
http://meetings.cshl.edu/courses/c-crys08.shtml
Deadline for applications: June 15th
This year
Jim,
The fact that liquid propane can exist at a range of temperatures is actually
a MAJOR advantage. While you must ensure that the temperature of the liquid
propane is just above its own freezing point, the very high boiling point of
propane ensures that there is liquid-to-solid contact wit
I would like to point out that flash-cooling in liquid propane has the
added complication that the liquid propane can have a range of temperature
and still be liquid. If you use propane you may not know which
temperature you are actually using. The temperature in the exposed layer
of the prop
Have you thought about phasing off the sulfurs? This is quite a common
technique nowadays.
Jim
On Tue, 27 May 2008, Joe Smith wrote:
Dear all,
Sorry for an off-topic query.
I have been unable to crystallize a Se-met containing protein (8 Met
in 206 amino acids) in the native crystallization
(CST)
From: Jim Pflugrath <[EMAIL PROTECTED]>
Subject: 2008 Rigaku Post-doc Summer Travel Bursary Awards
Rigaku Americas Corporation is pleased to announce the availability of five (5)
awards of $500 each to post-doctoral research fellows to help with the costs of
travel to upcoming
That's an easy hypothesis to test. Simply set up your drops with the same
conditions except without protein and see if you get crystals. Please let
us know the results. Thanks!
Jim
On Tue, 29 Apr 2008, Sam Stephenson wrote:
Are calcium citrate crystals a common false positive in trays with
I would use all the data myself and report that the model was built from a
a dataset with 74% completeness in the 2.25 to 2.15 Anngstrom shell. I
would not put the number 2.15 A in the manuscript title nor in the poster
title.
For me the acceptable completeness is 90% in the highest resolutio
Rigaku Americas Corporation is pleased to announce the availability of
five (5) awards of $500 each to post-doctoral research fellows to help
with the costs of travel to upcoming summer meetings such as the ACA
meeting in Knoxville, TN (May 31 - June 5), the IUCr meeting in Osaka
(August 23-31)
Hi everyone,
I received a lot of positive e-mails about my post on cryo
methods. One theme was, "Well, what are the papers I should read?"
I know of one such paper published in Methods. I have made the PDF of it
downloadable from our web site at http://www.rigaku.com/cryo/
Cheers,
Jim
There are many excellent review articles about cryocrystallography and
cryoprotectants. Do labs generally have these articles handy in a methods
folder? Do lab heads help their colleagues by making them read them?
Mineral oil is generally not a good oil to use because it changes volume
too m
Is there any way to do a search of crystal orientation matrices with a known
cell to find the best fit to the diffraction pattern? The data were collected
on the Pilatus6M detector so I am limited to mosflm and XDS for processing.
d*TREK will easily process Pilatus6M images.
Both packages alwa
Did you grow Malic Acid crystals?
I see no reason why glycerol cannot be the precipitant. I am aware that
at least one protein is crystallized with ethylene glycol as the
precipitant.
On Wed, 9 Jan 2008, JINJIN ZHANG wrote:
Dear All,
I have got large and nice crystals in a condition that
Bong angels are probably ideal already!
Please explain, so that I can teach this to my students. :) Jim
Folks, I wanted to call your attention to the following position(s)
available at Rigaku.
Thanks, Jim
Scientist/Programmer
Rigaku, the world's largest analytical X-ray company,
is seeking experienced scientific programmers to join
well-recognized Rigaku scientists such as Jim Pflu
It probably goes back to the days of using a single-counter diffractometer
where one didn't have multiple Bragg reflections on an image or film pack.
That is, each reflection was collected by itself. Even in a small molecule
crystal data collection nowadays, it would not hurt to have the crystal
c
Peter wrote:
You can edit these to reflect something that is available on the system - I
suspect that replacing the word "Adobe" with an asterisk might work, however
I haven't tried this myself (and I don't know how to easily query the fonts
that are available on the system - perhaps some X11
It has come to my attention that the wavelength of a Copper Kalpha may
have changed over the years. At least this appears to be true if you look
at the International Tables.
What is the currently approved wavelength in Angstrom of a Copper Kalpha
X-ray produced by a X-ray generator with a cop
Is there any advantage to bzip2-ing the individual images rather than
making one bzip2-ed tarball with tar cvfj?
Yes. If you have folks sending you images by sftp or e-mail, then you
don't have ensure a tarball of Giga or Tera bytes works. You can send the
smaller multiple files and restart
:
Really? How?
Jim Pflugrath wrote:
What about CrystalClear from Rigaku?
What about CrystalClear from Rigaku?
-Original Message-
From: Peter Zwart <[EMAIL PROTECTED]>
Date: Thu, 12 Jul 2007 08:55:04
To:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Program to 'visualize' the reciprocal space ?
> I don't think that there is a program available to do what
What is the mosaicity of the unfrozen crystal?
Jim
-Original Message-
From: Mary Fitzgerald <[EMAIL PROTECTED]>
Date: Mon, 9 Jul 2007 18:05:10
To:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help with reducing crystal mosaicity
Help please!
I'm looking for some new ideas. I have cr
I just wanted to re-post this in case you know someone who wants some
travel money. Jim
Rigaku Americas Corporation is pleased to announce the availability of five
(5) awards of $500 each to post-doctoral research fellows to help with the
costs of travel to upcoming summer meetings such as t
Rigaku Americas Corporation is pleased to announce the availability of
five (5) awards of $500 each to post-doctoral research fellows to help
with the costs of travel to upcoming summer meetings such as the ACA
meeting in Salt Lake City, Utah (July 21-26), the ECM meeting in
Marrakech, Morocco
X-ray Methods in Structural Biology
Cold Spring Harbor Laboratory
October 15th-30th, 2007
http://meetings.cshl.edu/courses/c-crys07.shtml
Deadline for applications: June 15th
This year marks the 20th time this course has been taught at Cold Spring
Harbor Laboratory. It is supported with funds
d*TREK does this - it's dtorient program works for any goniometer as
well. Or use CrystalClear which came with the detectors at U of Texas.
You probably have both these programs already.
Jim
On Mon, 21 May 2007, Bryan W. Lepore wrote:
are there any free programs which, given a diffraction ima
d*TREK from Rigaku can process these images.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Yanming Zhang
Sent: Wednesday, May 16, 2007 2:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] .sfrm image files
Hi, All,
I have image files with the format o
Although the peak height of S atoms can be used as an internal yardstick,
one has to worry about differences in occupancy and possibly hetergeneous
sites (i.e. Ca, Mn and Mg) which can confuse the interpretation of the
results.
On Mon, 16 Apr 2007, Eleanor Dodson wrote:
In cases like this I
Ethan, very nice web page. I like the discussion of required signal with
respect to one's diffraction experiment and counting statistics in the
results page.
I will use this in my lecture tomorrow on SAD/MAD phasing.
Do you mind putting Sulfur as one of the radio buttons?
Also, do you mind put
Hi Ian,
I am happy to read that your users trust d*TREK so much that they simply
click the buttons and away they go. The indexing program within d*TREK
now outputs the following text:
INFO - The above indexing solution is ONLY a hypothesis.
One must confirm the hypothesis by ex
Of course, the Rigaku system would be the best.
Jim
On Wed, 28 Feb 2007, Sankar Narayanan Manicka wrote:
Hi,
Our lab is planning to buy an X-ray machine for protein crystallography.
Which system would be best for home source, Oxford diffraction system
Xcalibur Nova or a MSC/Rigaku MicroMax-
See http://www.rigaku.com/protein/crystallization.html for a set of seven
favorites. Add bovine catalase to the list as well.
Jim
On Thu, 22 Feb 2007, Douglas L. Theobald wrote:
Hi all,
I'd like to pick the collective brain of crystallographers on this list --
what are some of the most eas
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