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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
