Besides the anomalous difference peak which might be similar in height to
the anom diff peak from an intrinsic sulfur found in cysteine or
methionine, also consider hydrogen bonding.
In general, a sulfate will not be donating a hydrogen bond. A phosphate
probably will.
##
The June 15th deadline for applications to the CSHL X-ray Methods in
Structural Biology Course to be held later this year, October 16 through
October 31, 2017 is rapidly approaching.
The official course announcement is here:
https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=17
so please pa
Let's step back a little bit first:
Do these 3 to 4 diffraction data sets (when kept separate) process nicely
individually and have good Rmeas and other results when scaled separately
from each other? If so, then do they also have the same unit cell
dimensions?
Jim
Date:Tue, 11 Apr 2017 1
I didn't see the figure, but I would not be surprised if cacodylate donates
a methyl group to make O-methylserine. Diethylene glycol is quite a bit
bigger than a methyl though.
Cacodylate is quite labile and undergoes radiolysis. It should probably
not be used for crystallization. If you either
Ooops, I forgot to mention that oils would be another way to keep the
crystal(s) on the loops. There are plenty of viscous sticky oils to choose
from. They are some of the same ones used when flash-cooling crystals.
-j
On Fri, Dec 23, 2016 at 12:17 PM, Jim Pflugrath
wrote:
> A couple of w
A couple of ways of shipping RT crystals:
We would mount in capillaries, seal the ends with wax, then Duco cement or
fingernail polish. Be aware that ambient air pressure will change alot
during the shipping process, so the plugs could be compromised. I would
take a box of pipetteman (or your fa
The June 15th deadline for applications to the CSHL X-ray Methods in
Structural Biology Course to be held later this year, October 12 through
October 27, 2015 is rapidly approaching.
The official course announcement is here:
https://meetings.cshl.edu/courses.aspx?course=C-CRYS&year=15
so please pa
Instead of Br which has a weak signal at its K edge, why not use Iodide at
some wavelength (or energy) where it gives a stronger signal? The longer
wavelength used will help with spot spatial resolution as well.
One may be fighting radiation damage, too.
One may be fighting a moving (vibrating?)
We have extended the application deadline for the CSHL X-ray Methods in
Structural Biology Course to be held October 13-28,2014.
Our earlier deadline was based on getting all the paperwork completed in
time for using NSLS, but since NSLS will not be available*, we can extend
the deadline to July 1
HKL-2000 has a menu button at the top "Report". If you click on that a report
is generated with mosaicity range explicitly listed.
It is probably not suitable to describe a crystal as having a single mosaicity
value because mosaicity may be anisotropic. It should be obvious that a unit
cell l
After all this discussion, I think that Bernhard can now lay the claim that
these 65 space groups should really just be labelled the "Rupp" space groups.
At least it is one word.
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Bernhard Rupp
The anomalous signal will always come from both Ca and S and any other atoms in
the crystal. One can determine whether an anomalous difference Fourier peak is
from a sulfur on a cysteine, methionine from the model, right? As for whether
a peak that is not part of an amino acid id Ca++ or Sulfu
should be above 0.80
There seems to be plenty of signal there with all values above 1.02. We have
solved structures with less multiplicity and lower .
There is a different criteria of "signal" for when you know the positions of
the anomalous substructure atoms and when you need to find the po
I think what one uses will depend on what one expects to be in the structure
and the resolution and the quality of their diffraction data.
I usually start with 1.8 Å resolution data in case there is chance of having
disulfides. Then 1.9, then 2.4, then 2.0, then 2.6, then 2.2, then 1.85, then
Further to what Nat wrote which I completely agree with, you should tell us the
following:
1. Expecting signal of a Calcium atom and expected signal of a Magnesium atom.
2. Are there any intrinsic anomalous scatterers in the structure that you trust
such as sulfurs from methionines and cysteine
And what if the site(s) is(are) a mixture of bound metal ions? What if Mg++,
Ca++, Na+, Mn++, et al. are bound at the same site(s)? Can the diffraction
data rule that out?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Faisal Tarique
[faisalta
If one is using the HKL GUI, then click on the menu bar button "Report" and
read the report that is generated.
One caveat is that HKL will count any systematically absent reflections in the
input files as part of the total number of observations. I forget if scalepack
counts the systematically
Thanks for the clarification. I thought at first this position might be
related to Dance Your PhD.
http://news.sciencemag.org/scientific-community/2013/11/dance-your-ph.d.-and-winner-…
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sebastian
I think you are talking about the R of the reflections in an image to the set
of unique reflections resulting from scaling.
Here is a definition of Rmerge from a dtscaleaverage log file:
In the tables below Rmerge is defined as:
Rmerge = Sum Sum |Ihi - | / Sum Sum
h i
If one is mounting in glass capillaries, we used to put them in a box of blue
tips (1000 ul pipetteman tips). Just put a small rolled up wad of kimwipe down
in the bottom, so that the capillary does not jam itself down in the narrowing
of the tip point. Every capillary gets its own tip and one
Clearly, it is always possible to do non-cryogenic data collection simply by
not using a cryogenic cooling device and mounting crystals so that they do not
dehydrate or dry out.
I've been doing quite a lot of room temperature data collection lately because
in the home lab we can SAD-phase lysoz
And quick iodide soaks may be useful in the 200 mM range. See the sped-up
video:
http://www.youtube.com/watch?v=45Qc3jOPaKY
Quiz time: What wavelength would give iodide a similar signal to that of
selenium? Can one get a better signal than selenium by choosing a different
wavelength for data
Hi Roger,
We have a simple lysozyme project where we collect diffraction images in less
than 30 seconds total exposure time and solve the structure by SAD phasing.
I've thought that this might make an ideal lab practical: grow crystals one
week, everyone collects the data on their own crystal
Here's an easy experiment to try:
What happens when you flash-cool your reservoir solution in Liquid Nitrogen?
Does it remains "glass-clear" at 100 K or lower?
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of abhimanyu singh
[abhising
Graeme wrote:
"... Rpim is much more instructive. ... as each of these tells something
different."
I have to ask:
"Why is Rpim much more instructive? I'm trying to figure this out still. Can
one please summarize what are best practices with all these numbers and how
each of these tells someth
Please tell me why Rpim should be looked at. Cannot one have meaningless data
and have lots of multiplicity to drive Rpim lower without any real benefit?
Under what conditions is Rpim useful?
And suppose one looks at (and not /) and CC1/2. What of it?
And let me write what Phil wrote in a s
The current version of scalepack already calculates CC1/2 and reports it in the
log file.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Francesco
Angelucci [francesco.angelu...@uniroma1.it]
Sent: Wednesday, September 18, 2013 5:21 AM
To: CCP4BB@
I have to ask flamingly: So what about CC1/2 and CC*?
Did we not replace an arbitrary resolution cut-off based on a value of Rmerge
with an arbitrary resolution cut-off based on a value of Rmeas already? And
now we are going to replace that with an arbitrary resolution cut-off based on
a value
I wonder if the "rejects" file had a large number of reflections in it in one
case, but not in the other case. One can be playing with various options and
create or add to such a large list. That's why there is the "Delete Reject
file" option.
Jim
Fro
How does that compare to something that readily works with Fe, such as horse
hemoglobin on a home lab copper X-ray system with 2 Fe in 291 residues in the
asymmetric unit?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Edward A. Berry
[be
If one has cryoprotectant in their conditions, one may be surprised that
crystals can grow at -20 deg C and probably lower. Practice with lysosyme. :)
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Glenn Masson
[glennmas...@gmail.com]
Sent: Thurs
Hey Everybody,
I wanted to draw your attention again to the upcoming application deadline on
June 15, 2013 for the
CSHL X-ray Methods in Structural Biology Course to be held October 14-29, 2013.
Also please also pass this on to any colleagues, friends, professors, research
associates, grad stud
"Precision does not trump accuracy" is something Michael Blum told me.
Also Charles Wheelan wrote in his recently published "Naked Statistics": “But
no amount of precision can make up for inaccuracy.”
I myself have been pleasantly surprised at how low multiplicity can be nowadays
and still d
Most participants in the CSHL X-rays Methods in Structural Biology course have
seen the powerpoint presentation of Alex McPherson's trip to Mars in 2001.
Here are a couple of slides from the presentation:
http://i43.tinypic.com/33kx79l.jpg
http://i39.tinypic.com/oic17r.jpg (Trehalose was pretty
Maybe you crystallized something else? Did you look up that unit cell in the
PDB?
I am having a few issues with a data set I have been working on recently, and
was hoping to get some ideas on how to deal with it, if anyone is in the mood.
.
I think James gets to 'fight' like in the old game of rogue by pressing the h,
j, k, l keys on his keyboard (not a detachable one either). While Eugene gets
to use a modern game controller or a Wii.
Ooops, game is already over and James has lost.
Jim
From: CC
As mentioned lots of reasons for this.
a. Poor crystal
b. Poor mount of the crystal
c. Poor equipment or non-working equipment
d. Poor maintenance of good equipment
e. Improper cryoprotection
f. Vibration or movement of goniometer, goniometer head, mounting pin, mounting
loop, magnet, etc
g. Temp
5 degrees per image may be problematic for some algorithms since the
diffraction spots have uncertain positions in three dimensions. Two dimensions
will come from the position of the spot on the detector and the position of the
detector. The third dimension will come from the rotation angle va
If one tries to use a dye to determine if crystals are protein or salt, then I
recommend that they use both a positive and a negative control. So have some
handy salt or sugar crystals ready along with some known protein crystals to
use as controls.
Jim
From:
A number of protein crystal recipes are available on the Rigaku web site:
http://www.rigaku.com/products/protein/recipes
Lysozyme is nice because it is so cheap, grows quickly, cryoprotectants in a
straightforward way, and the unit cells are not large nor are the crystals
fragile. One can get t
Suggestion: What does your plunge of a loopful of the buffer (no crystal) into
liquid nitrogen tell you?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Yuri Pompeu
[yuri.pom...@ufl.edu]
Sent: Friday, November 30, 2012 7:22 PM
To: CCP4BB@JI
Sucrose co-crystallized in lysozyme is wonderful. I think a soak will crack the
crystals, but sometimes not.
Here's a pic of electron density from an orthorhombic crystal of lysozyme
solved in the recent 2012 CSHL X-ray Methods in Structural Biology course:
http://i46.tinypic.com/2e4xk7k.jpg
I was asked by our shipping folks what we should put on the Customs Declaration
so that samples that we ship or that are shipped to us (in dewars, styrofoam
boxes, and/or padded envelopes) would not be held up in Customs.
I had them put:
"Scientific samples of less than 1 mg of non-infectious
This looks like an output from SCALEPACK. Unfortunately, one has no way to
know from the output if 21 and 90 are strong intensities or not. One cannot go
by the I/sigmaI alone. For example, suppose there is thermal diffuse scatter
at these positions or perhaps there is a cosmic ray or radioac
In my opinion Rpim is not related directly to anomalous signal, so perhaps that
is why there is some confusion.
Also I think some folks confused Rpim with Rrim. The latter is also called
Rmeas. But once again, these are not related directly to anomalous signal. I
do not find Rpim very useful
How would you distinguish between a mixture of Ca and Zn in the same locations?
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Kumar, Veerendra
[veerendra.ku...@uconn.edu]
Sent: Tuesday, October 30, 2012 1:55 PM
To: CCP4BB@JISCMAIL.AC.UK
Su
d*TREK can process single crystal diffraction images from all the common
detectors including not only Rigaku detectors, but many different detectors
found at synchrotron beamlines around the world such as the APS, ALS, NSLS,
CHESS, SLS, ESRF, Diamond, Soleil, PhotonFactory, SPring8, CAMD, Triest
Oops, I meant if the variance of the X-ray background is exactly zero (and not
if the X-ray background is zero). Think about that in the context of Poisson
counting statistics. :)
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jim Pflugrath
Singly-measured reflections should have a sigma from Poisson counting
statistics, so that should not be a problem. A problem might occur if the
X-ray background is exactly zero and the observed (sic) intensity is exactly
zero.
From: CCP4 bulletin board [CCP4BB
A high school intern of mine made one to show the next year's interns. We have
not posted to youtube, but perhaps we should. You also could make one
yourself in about 5 minutes. :)
We have posted a youtube video on how to use cryotongs:
http://www.youtube.com/watch?v=ikiF2qpCRKs
Jim
__
For large unit cells, one must take particular care with the X-ray beam and the
orientation of the crystal. The latter has already been mentioned in previous
response. For the beam, some things to do are:
1. Make crystal smaller.
2. Make beam smaller (use a smaller collimator size).
3. Reduce b
Sucrose, sorbitol, Splenda, trehalose, etc, but instead of 25% (is that w/v or
v/w?), try using 100% saturated in reservoir, 75% saturated in reservoir, or
50% saturated in reservoir. You will have to TEST these. See also this
webinar on cryocrystallography which shows how to make these soluti
And for more Personal Reflections, one may wish to take a gander at the Rigaku
Webinar series with presentations by Brian Matthews and Michael G. Rossmann.
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Carter, Charlie
[car...@med.unc.edu]
S
Once again I wanted to draw everyone's attention to the
Cold Spring Harbor Laboratory 2012 X-ray Methods in Structural Biology
course which will take place
October 15 through October 30, 2012.
The official course announcement is here:
http://meetings.cshl.edu/courses/c-crys12.shtml
I think the
As with all reagents used in the lab it is best to understand the health
hazards. Thanks for note.
Jim
From: Jacob Keller [j-kell...@fsm.northwestern.edu]
Sent: Monday, May 21, 2012 5:22 PM
To: Jim Pflugrath
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb
Here is a trick which I will attribute to Cambridge:
Fill balloon with gas. Put end of balloon over 15 ml Falcon tube. Put Falcon
tube in LN2. No wasted gas.
I would recommend CF4 or carbon tetrafluoride instead of propane though. CF4
is cheap and non-dangerous.
Jim
_
Please see my poster at the ACA 2012 meeting. See also:
(1) Dauter, Z., Dauter, M. & Rajashankar, K.R. (2000) Acta Cryst. D56, 232-237.
(2) Nagem, R.A.P, Dauter, Z. & Polikarpov, I. (2001) Acta Cryst. D57, 996-1002.
:)
From: CCP4 bulletin board [CCP4BB@JISCMAIL.A
Iodide is a fantastic derivative. One does not need a lot with modern X-ray
equipment, careful data collection, and great software.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rajesh Kumar
[ccp4...@hotmail.com]
Sent: Thursday, May 03, 2012 8:5
Rigaku ACTOR robots can accept many different styles of pucks depending on the
LN2 dewar baseplate that the particular ACTOR is equipped with. Rigaku in
China will sell ACTOR pucks, but if you are looking for ALS-style pucks or
ESRF-style pucks or Unipucks or ???, then I am not sure where to ge
I am aware that some programs report interesting numbers.
In addition to what Andrew wrote about resolution cutoffs and "truncated"
reflections, I'd like to mention another issue with systematically absent
reflections.
The number of observations or reflections that come from an integration prog
The first Rigaku R-AXIS IIC in North America were installed in late 1990 at
Yale University and McMaster University. That's the same year the Hubble
Telescope went into space and the first search engine Archie was released.
The last R-AXIS IIC shipped in 1994. So these are really vintage syste
In addition to reducing the beam divergence, you may wish to use a smaller beam
size by using a smaller collimator or making the slits smaller. A smaller
crystal can also help to spatially separate the Bragg spots as can moving the
detector closer to the crystal. Yes, closer to the crystal. Th
There could be many causes for this. Perhaps you do not have the best def.site
file for your detector / beamline / hardware. What do your local HKL2000
experts tell you?
You could e-mail me an image and I can help you.
Jim
From: CCP4 bulletin board [C
Just a thought for those that mentioned propane and ethane, I would like to
suggest that they try carbon tetrafluoride (CF4) instead. It certainly should
be much safer. It melts at 90 K and boils at 145 K, so you know you are below
145 K if you see it as a liquid.
When you crystallized your lysozyme, did you have any other anomalous
scattering atoms in the conditions? I am thinking of chloride ions in
particular, but there could be many others. How did you distinguish between
sites of xenon and sites of other kinds of atoms in your analysis?
Did you do
Folks may wish to watch a webinar I gave on using HKL3000. In the webinar I
describe how to calculate an Rmeas from scalepack output and also discuss a few
other "how-to" operations.
See www.rigaku.com/protein/webinars-past.html for more viewing pleasure.
Jim
___
If you edit the PDB file "by hand", then you should have no problems. Some
folks might cringe at this, but this does work:
1. Like Roger Rowlett said, "place atom at pointer". You can place a chloride
there. Be sure to add to your molecule and not a new molecule.
2. Save the coordinates to a
Any cacodylate buffer will cause gas to be produced. One only needs a minute
exposure on a modern home lab source to see this happening. I suggest that
everyone avoid cacodylate in their crystallization drops that end up being
exposed to X-rays.
Jim
F
A source of confusion is that we are using two different definitions of
"origin". In the a graphics program sense (coot, pymol), the origin is always
at xyz coordinate (0, 0, 0). I think that's what Napo means by "present the
same cell and origin."
However, imagine a crystal upon which we pu
All the currently used diffraction image processing programs can tell the
crystal orientation from a single diffraction image.
Some programs like d*TREK can calculate new orientations for the crystal if the
crystal is mounted on a reasonable goniometer such as the Rigaku Kappa
goniostat or the
For some ideas on cryocrystallography, one can watch an online webinar on the
subject:
http://www.rigaku.com/protein/webinar-001.html
Maybe some "unbiased" folks can comment? ;)
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Leonard
PEGs have small amounts of anti-oxidants added to them by the manufacturer.
I think different manufacturers may use different compounds.
And you might imagine that PEGs themselves with their -OH groups go from
alcohol to adelhyde to carboxylate.
-Original Message-
From: CCP4 bulletin boa
Many programs such as d*TREK (free download) can predict the actual reflns
that would appear on detector given a particular experiment (crystal,
spacegroup, unit cell, detector, detector position, wavelength, etc).
A quick prediction shows that one will get about 3.9-fold redundancy with
the rotat
There is always an anomalous signal to be seen if one measures things well
enough. One does not need to be at the edge in order to detect anomalous
scatterers. For example, most (if not all) of the sulfur SAD phasing is
done well away from the sulfur edge.
I will note that you stated that the f
For each observation or measurement, HKL, d*TREK, and all other common
programs to my knowledge add up the bits of each relfection from its parts.
They do not add parts of of other reflections (even if symmetry-related)
into a reflection. Reflections for which only part of the Bragg peak is
measur
OK, same space group, but you didn't indicate what the unit cells were.
They are different, right?
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ferrol
shariff
Sent: Sunday, July 10, 2011 3:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Same protein, different
Please clarify:
Did you process the sets separately from the images?
Or did you process 360 degrees of images all the way to scaled, but
unaveraged results, then average reflections from the 5 different rotation
ranges?
Or something else?
With most processing programs that I am aware of, one ca
I would be very careful about any bond to As. I would imagine such
bonds would be very susceptible to radiolysis with typical radiation used
in the diffraction data collection. Have you performed some
diffraction experiments of various time lengths (or flux) and seen what
happens around this
Instead of an imperfect crystal, this can also occur if one chooses the
wrong Bravais lattice type (or spacegroup) to integrate. For example, if
you choose tetragonal when it is really orthorhombic with a ~ b, or if you
choose orthorhombic and beta is 90.2, then you can see that trying to force
th
If you make your images available via ftp, I can take a closer look and come
up with plausible explanations and fixes.
Did you lock down the phi-axis?
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of bie
gao
Sent: Wednesday, June 22, 2011 11:23 AM
To: CCP4BB@JISCMA
Since Frank mentioned cryotongs, I wanted to point to a video of their use
on youtube:
http://www.youtube.com/watch?v=ikiF2qpCRKs
Jim
On Wed, 8 Jun 2011, Frank von Delft wrote:
Hi Zhijie --
With all manipulations on the goniometer, I strongly advise what I learnt
from Elspeth Garman: pra
I wanted to draw everyone's attention to the Cold Spring Harbor Laboratory
2011 X-ray Methods in Structural Biology course which will take place
October 17 through November 1, 2011.
The official course announcement is here:
http://meetings.cshl.edu/courses/c-crys11.shtml Astute viewers of that lin
I always try sugars for everything. There is a cryocrystallography webinar
at rigaku.com with embedded videos on how to do this. 50% to 100% saturated
sugar (sucrose, glucose, trehalose, sorbitol, et al.) in reservoir buffer is
usually what I try. :)
-Original Message-
From: CCP4 bulleti
Yes, reciprocal lattice coordinates are available for reflections with
d*TREK.
My colleague has also written a "reciprocal lattice viewer" which takes
image pixels and transforms them to a reciprocal lattice. I'm sure others
have similar programs.
But in this modern internet age, I would say enli
In general, the Rmerge and Rmeas should get better with a lower symmetry
spacegroup, so that's weird.
Maybe you didn't crystallize what you thought you crystallized. Do people
runs gels anymore on crystals to get an idea of what's in the crystal or do
they do MassSpec?
I think another way to go
This link should be helpful to many folks here:
http://blog.revolutionanalytics.com/2011/04/250-years-of-bayes-theorem.html
Frances Jurnak published a paper in 1986 on PEG impurities and purification.
As I recall, it turns out that different manufacturers put different
additives in PEGs as preservatives. These are generally anti-oxidants.
PEGs do get oxidized.
I suggest you heat up your new PEG solutions to say 80 d
Collect all your diffraction data in your home lab, solve the phase problem,
fit the map, refine, deposit coordinates in the PDB.
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Careina Edgooms
Sent: Friday, March 25, 2011 2:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject:
Glycerol is just another additive to crystallizations and a reasonably good
cryoprotectant. Sometimes it helps to grow crystals, sometimes it has no
effect, and sometimes it interferes with crystal growth. Have I covered all
the possiblities?
One thing is the glycerol often makes a protein more
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) and not /.
A review of similar articles in the same journal will show what is typical
for the journal. I think you will find that the cutoff varies.
This information can be used in your response to the r
I will offer my view.
I hate stereo glasses and hate stereo in general.
One should be able to see 3D from the depth-cueing and by keeping the view
in motion. For fitting, I like to flip the view by 90 degrees. I know I am
going to move in displayX and displayY, but never in displayZ. I then
If you make the images available, maybe I can take a look and try to use
d*TREK. You will need to be selective about the spots used in indexing.
Most programs can add or delete spots manually.
You may wish to make the X-ray beam smaller and try to expose only a small
volume of one of the crystals.
Cool the coverslip on the opposite side of the crystal with a chip of dry
ice. Do not freeze the drop. I learned this from Gary Gilliland. Also I
wonder if you can simply move the whole tray into a cooler temperature?
You can imagine that the thermal expansion coefficient of the glass
cover
You should know that your crystal mosaicity is a physical property of your
crystals and the diffraction experiment. Generally, it is anisotropic
though most programs output a single value. How can that single value
describe what is really happening in your experimental data?
You can do anything
Crystals of tendamistat were grown from hydrochloric acid and solved by MIR.
I do not recall anything special about the heavy atom soaks, so try
everything in your heavy atom closet.
What have you tried that has not worked?
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On B
With Izit or other dyes, you might wish to do a positive control with bona
fide protein crystals and a negative control with bona fide salt crystals.
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Matthew Bratkowski
Sent: Tuesday, November 16, 2010 7:58 PM
To: CC
In general, if the Rmeas or Rmerge is high in the low resolution shells,
then something is not optimal with the data collection.
Bill Shepard has already mentioned the loop vibrating or moving in the
cryogenic gas flow. Other problems could be the goniometer head was loose,
the magnet was loose,
It reads like you need to run a lane or two with a positive control of some
kind. Can you grow lysozyme, glucose isomerase, hemoglobin or other
crystals of a protein around the same expected molecular weight and try run
on the gel lanes with about the same amount of crystalline volume as your
puta
Are these very strong reflections? Do they appear on more than one image?
Are they an artefact of the detector or the image display program?
Zbyszek,
Since you mention I/sigmaI in your PDF, do you mean or
/?
Do you mean I/sigmaI (in whatever rendition you choose) for the averaged
unique reflections or the I/sigmaI for the observations?
Also since one can adjust sigmaI in your scalepack program through the use
of the Error Scale Fac
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