Re: [ccp4bb] neutron data measurement

2011-09-23 Thread Leif Hanson
This thread caught my attention several days ago and I now have enough time
to add my two cents worth. These are my own biases and probably do not
reflect the views of my friends and colleagues at various neutron
facilities.


With respect to the size of crystals for neutron diffraction, a good rule of
thumb is that there should be at least 10exp24 uniformly ordered unit cells
in a D2O exchanged crystal to have successful diffraction on par with
rotating anode data measured on a crystal with a tenth the volume. Several
data sets have been measured from smaller crystals, and perdeuteration
lowers the volume needed to extract useful information. Most of the neutron
data has a resolution cutoff of 1.8 to 2.0Å, which permits unambiguous
placement of deuterons and solvent molecules, especially when completing
dual refinement of X-ray and neutron data from the same crystal.


There have been a limited number of low temperature neutron diffraction
experiments for several reasons. First, of the available neutron beamlines
for macromolecular data measurement there are only one or two with open flow
cryostats available, limiting the locations for standard macromolecular
cryocrystallography. Second, there are a tremendous number of important
structures that can be done at room temperature. It is difficult to justify
the time needed for low temperature work to experimental review panels when
crystals are available to resolve a knotty enzyme mechanism problem. Third,
the size of crystal needed for successful neutron diffraction is right at
the limit of the size of crystal that can be successfully flash-cooled
without inducing excess mosaicity. Most neutron beamlines use some form of
quasi-Laue data collection strategy. Mosaicities in excess of 0.5º render
most crystals unusable for neutron data measurement. Remember that a lot of
uniform unit cells are needed to get a usable diffraction signal from
neutrons. Often a large flash-cooled cooled crystal appears to have low
mosaicity when exposed to 0.5mm x-ray beam. However, when placed in the 3mm
neutron beam, limited streaky low-resolution diffraction appears. It is
difficult to judge the quality of flash-cooled neutron diffraction sized
crystal without placing it in the neutron beam. Returning to point 2 it is
difficult justify the time needed on fishing expedition. So far the only
large crystals I have been able to flash-cool that met the demands of size
and crystal perfection had very low solvent content or were grown in high
levels of cryoprotectant. That said, several critical problems cry out for
low temp neutron studies so there is every reason to persevere. I would be
pleased to answer any questions off-line for those of you with more interest
in neutron cryocrystallography.


Finally with respect to radiation damage, Benno Schoenborn has had a
myoglobin crystal in sealed capillary that he has used as a “standard
candle” for testing neutron beamlines. There has been no discernable
degradation of the crystal in all the years he has used it. The neutrons
used for neutron diffraction are ‘cold’ neutrons, usually with energies of 1
– 10 meV. Damage could come from activated nuclei, but these are usually
very limited on a molar basis within the crystal. As can be seen with
Benno’s myoglobin crystal, 30 years of iron activation has yet to produce a
measurable defect.


Leif Hanson

University of Toledo


Re: [ccp4bb] neutron data measurement

2011-09-23 Thread Patrick Shaw Stewart
 Third, the size of crystal needed for successful neutron diffraction is
right at the limit of the size of crystal that can be successfully
flash-cooled without inducing excess mosaicity.

Can't the crystal be flash-cooled at high pressure? The inventors of the
Crystal Harp in Zurich use a machine that does this automatically for cryo
e.m., which many universities already have.



On Fri, Sep 23, 2011 at 4:40 PM, Leif Hanson leif.han...@gmail.com wrote:

 This thread caught my attention several days ago and I now have enough time
 to add my two cents worth. These are my own biases and probably do not
 reflect the views of my friends and colleagues at various neutron
 facilities.


 With respect to the size of crystals for neutron diffraction, a good rule
 of thumb is that there should be at least 10exp24 uniformly ordered unit
 cells in a D2O exchanged crystal to have successful diffraction on par
 with rotating anode data measured on a crystal with a tenth the volume.
 Several data sets have been measured from smaller crystals, and
 perdeuteration lowers the volume needed to extract useful information. Most
 of the neutron data has a resolution cutoff of 1.8 to 2.0Å, which permits
 unambiguous placement of deuterons and solvent molecules, especially when
 completing dual refinement of X-ray and neutron data from the same crystal.


 There have been a limited number of low temperature neutron diffraction
 experiments for several reasons. First, of the available neutron beamlines
 for macromolecular data measurement there are only one or two with open flow
 cryostats available, limiting the locations for standard macromolecular
 cryocrystallography. Second, there are a tremendous number of important
 structures that can be done at room temperature. It is difficult to justify
 the time needed for low temperature work to experimental review panels when
 crystals are available to resolve a knotty enzyme mechanism problem. Third,
 the size of crystal needed for successful neutron diffraction is right at
 the limit of the size of crystal that can be successfully flash-cooled
 without inducing excess mosaicity. Most neutron beamlines use some form of
 quasi-Laue data collection strategy. Mosaicities in excess of 0.5º render
 most crystals unusable for neutron data measurement. Remember that a lot of
 uniform unit cells are needed to get a usable diffraction signal from
 neutrons. Often a large flash-cooled cooled crystal appears to have low
 mosaicity when exposed to 0.5mm x-ray beam. However, when placed in the 3mm
 neutron beam, limited streaky low-resolution diffraction appears. It is
 difficult to judge the quality of flash-cooled neutron diffraction sized
 crystal without placing it in the neutron beam. Returning to point 2 it is
 difficult justify the time needed on fishing expedition. So far the only
 large crystals I have been able to flash-cool that met the demands of size
 and crystal perfection had very low solvent content or were grown in high
 levels of cryoprotectant. That said, several critical problems cry out for
 low temp neutron studies so there is every reason to persevere. I would be
 pleased to answer any questions off-line for those of you with more interest
 in neutron cryocrystallography.


 Finally with respect to radiation damage, Benno Schoenborn has had a
 myoglobin crystal in sealed capillary that he has used as a “standard
 candle” for testing neutron beamlines. There has been no discernable
 degradation of the crystal in all the years he has used it. The neutrons
 used for neutron diffraction are ‘cold’ neutrons, usually with energies of 1
 – 10 meV. Damage could come from activated nuclei, but these are usually
 very limited on a molar basis within the crystal. As can be seen with
 Benno’s myoglobin crystal, 30 years of iron activation has yet to produce a
 measurable defect.


 Leif Hanson

 University of Toledo




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