Once upon a time, quite a while ago, a group of us went to a synchrotron (which shall remain nameless) to collect data. When we arrived, we found that due to circumstances beyond our control, or our host's control, the hutch was empty - no diffractomer, no controls.
We decided to take this as a challange and installed the equipment needed to collect data and indeed collect some data, all in the timeframe of 5 days. Technically, that would be 5*8*3 hours, of course.
One of the things learned that all of us will never forget is this: our X-ray wavelength was not what we thought it was and the only way to resolve that issue was to put something in the beam with a known (powder) diffraction pattern. When you know the distance between your sample and detector accurately, everything else follows.
There are quite a few choices you might consider, and water never occurred to us at the time because we did not have freezing capabilities. A capillary with crushed salt (NaCl) crystals works (and will be good for a long time, provided you do not brake it). Most polymers work and most wax samples you would use for sealing capillaries work. Basically anything that is crystalline in nature works.
It is probably best to try your experiment at room temperature (stick a piece of cardboard on the coldstream nozzle for 5 minutes) so you won't have to worry about cell parameter change with temperature. If you have a lab source and detector, you can determine ahead of time (and convince yourself) which sample you want to pack in your synchrotron kit and never remove again. It is worth carrying.
Mark
Mark van der Woerd
BAE SYSTEMS
Huntsville, AL
-----Original Message-----
From: Edward Berry <[EMAIL PROTECTED]>
To: CCP4BB <[email protected]>
Sent: Tue, 29 Nov 2005 11:54:47 -0800
Subject: [ccp4bb]: ice lattice parameters - was: WHATCHECK Deformation Matrix - is it advisable to c orrect the cell ?
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*** CCP4 home page http://www.ccp4.ac.uk ***
I gather the consensus is that we should calculate our cell constants
assuming the wavelength and crystal-to-film distances are accurate,
rather than refine them based on what-check output. But if we don't
quite trust these values (say on our in-house equipment; of course
the beamline values will be bang-on) it seems to me that ice spots
and rings would make a good calibration check, if we know the
correct values for the ice lattice parameters to high accuracy.
This can usually be applied "a posteriori", as most data collection
trips will probably contain at least one shot of a crystal with
ice rings, or at least a few spots due to ice toward the end of
a run (which makes the tell-tale peaks in the wilson plot at 2.26
and 2.08 nm if they fall close to predicted protein diffraction spots).
Or you can freeze a loop of distilled water and take a shot after
collecting your best crystal, without changing wavelength or distance.
But then silver behenate may be better.
Programs exist for fitting diffraction rings, usually to determine
the beam center, but an accurate resolution is also output.
I found lattice parameters for hexagonal ice in one of the international
tables: (a=b= 4.5212, c=7.3666 A), and calculated spacings
3.915, 3.683, 3.457, 2.683, 2.456, 2.261, 2.161, 2.080, and 1.958.
Does anyone have accurate values for these spacings at 100K?
What is the temperature dependence?
Sometimes I get rings at different spacings, which I suspect are
due to another crystal form of water. The triplet around 3A
is replaced by a single ring at 3.23. What are the lattice parameters
for this stuff?
Dirk Kostrewa wrote:
> Hi Jorge,
> > I stumbled across the same deformation matrix problem reported by > WHATCHECK a couple of years ago and initiated a little discussion on the > CCP4BB, at that time assuming a bug in the program. However, from > discussions with the author of WHATCHECK, Gerd Vriend, it turned out > that apparently this deformation matrix resulted from slightly different > implementations of the same (!) Engh & Huber parameters in WHATCHECK > and, by that time, in XPLOR/CNS. I can't remember anymore, which of the > bond lengths came out slightly different. But let's assume, that the C=O > bonds on average come out slightly longer in your refinement program > compared to the library used by WHATCHECK (there are some doubts about > the correct length of the C=O bond in E&H). If you don't have a single > (anti-)parallel helix bundle or beta-sheet as the only structural > feature of your protein in the unit cell, then the directions of the > C=O-vectors should be more or less equally distributed with respect to > your coordinate system, meaning that also all components of these > vectors along the unit cell axes should occur with about equal > frequencies. A systematic comparison of the on average too long C=O-bond > lenghths with the WHATCHECK library value would then suggest, that your > unit cell dimensions should be decreased by a few percent, so that after > orthogonalization the refined C=O bonds come out with the "correct" > slightly shorter average length (I hope, it's not the other way around > ;-) ). I can't tell you exactly how WHATCHECK does its analysis, because > the web-site is currently not reachable. As long as the data processing > was done with great care, personally, I would trust the refined unit > cell parameters more than the "deformation matrix" analysis by WHATCHECK.
> Regarding your question about cryo-temperature bond lenghts, I think, it > would be time to do a new analysis of ideal bond lenghts of now many > more very high resolution protein structures whose crystals were > measured at cryo-temperature to complement the Engh & Huber parameters.
> (hexagonal, a=b= 4.5212, c=7.3666 A)
Sorted by resolution
n h k l d()
1 0 0 1 7.367
2 1 0 0 3.915
3 0 0 2 3.683
4 1 0 1 3.457
5 1 0 2 2.683
6 0 0 3 2.456
7 1 1 0 2.261
8 1 1 1 2.161
9 1 0 3 2.080
10 2 0 0 1.958
11 1 1 2 1.927
12 2 0 1 1.892
13 0 0 4 1.842
14 2 0 2 1.729
15 1 0 4 1.667
16 1 1 3 1.663
17 2 0 3 1.531
18 2 1 0 1.480
19 2 1 1 1.451
20 1 1 4 1.428
21 2 1 2 1.373
22 2 0 4 1.341
23 3 0 0 1.305
24 3 0 1 1.285
25 2 1 3 1.268
26 3 0 2 1.230
27 2 1 4 1.154
28 3 0 3 1.152
29 2 2 0 1.130
30 2 2 1 1.117
*** CCP4 home page http://www.ccp4.ac.uk ***
I gather the consensus is that we should calculate our cell constants
assuming the wavelength and crystal-to-film distances are accurate,
rather than refine them based on what-check output. But if we don't
quite trust these values (say on our in-house equipment; of course
the beamline values will be bang-on) it seems to me that ice spots
and rings would make a good calibration check, if we know the
correct values for the ice lattice parameters to high accuracy.
This can usually be applied "a posteriori", as most data collection
trips will probably contain at least one shot of a crystal with
ice rings, or at least a few spots due to ice toward the end of
a run (which makes the tell-tale peaks in the wilson plot at 2.26
and 2.08 nm if they fall close to predicted protein diffraction spots).
Or you can freeze a loop of distilled water and take a shot after
collecting your best crystal, without changing wavelength or distance.
But then silver behenate may be better.
Programs exist for fitting diffraction rings, usually to determine
the beam center, but an accurate resolution is also output.
I found lattice parameters for hexagonal ice in one of the international
tables: (a=b= 4.5212, c=7.3666 A), and calculated spacings
3.915, 3.683, 3.457, 2.683, 2.456, 2.261, 2.161, 2.080, and 1.958.
Does anyone have accurate values for these spacings at 100K?
What is the temperature dependence?
Sometimes I get rings at different spacings, which I suspect are
due to another crystal form of water. The triplet around 3A
is replaced by a single ring at 3.23. What are the lattice parameters
for this stuff?
Dirk Kostrewa wrote:
> Hi Jorge,
> > I stumbled across the same deformation matrix problem reported by > WHATCHECK a couple of years ago and initiated a little discussion on the > CCP4BB, at that time assuming a bug in the program. However, from > discussions with the author of WHATCHECK, Gerd Vriend, it turned out > that apparently this deformation matrix resulted from slightly different > implementations of the same (!) Engh & Huber parameters in WHATCHECK > and, by that time, in XPLOR/CNS. I can't remember anymore, which of the > bond lengths came out slightly different. But let's assume, that the C=O > bonds on average come out slightly longer in your refinement program > compared to the library used by WHATCHECK (there are some doubts about > the correct length of the C=O bond in E&H). If you don't have a single > (anti-)parallel helix bundle or beta-sheet as the only structural > feature of your protein in the unit cell, then the directions of the > C=O-vectors should be more or less equally distributed with respect to > your coordinate system, meaning that also all components of these > vectors along the unit cell axes should occur with about equal > frequencies. A systematic comparison of the on average too long C=O-bond > lenghths with the WHATCHECK library value would then suggest, that your > unit cell dimensions should be decreased by a few percent, so that after > orthogonalization the refined C=O bonds come out with the "correct" > slightly shorter average length (I hope, it's not the other way around > ;-) ). I can't tell you exactly how WHATCHECK does its analysis, because > the web-site is currently not reachable. As long as the data processing > was done with great care, personally, I would trust the refined unit > cell parameters more than the "deformation matrix" analysis by WHATCHECK.
> Regarding your question about cryo-temperature bond lenghts, I think, it > would be time to do a new analysis of ideal bond lenghts of now many > more very high resolution protein structures whose crystals were > measured at cryo-temperature to complement the Engh & Huber parameters.
> (hexagonal, a=b= 4.5212, c=7.3666 A)
Sorted by resolution
n h k l d()
1 0 0 1 7.367
2 1 0 0 3.915
3 0 0 2 3.683
4 1 0 1 3.457
5 1 0 2 2.683
6 0 0 3 2.456
7 1 1 0 2.261
8 1 1 1 2.161
9 1 0 3 2.080
10 2 0 0 1.958
11 1 1 2 1.927
12 2 0 1 1.892
13 0 0 4 1.842
14 2 0 2 1.729
15 1 0 4 1.667
16 1 1 3 1.663
17 2 0 3 1.531
18 2 1 0 1.480
19 2 1 1 1.451
20 1 1 4 1.428
21 2 1 2 1.373
22 2 0 4 1.341
23 3 0 0 1.305
24 3 0 1 1.285
25 2 1 3 1.268
26 3 0 2 1.230
27 2 1 4 1.154
28 3 0 3 1.152
29 2 2 0 1.130
30 2 2 1 1.117
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