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Another point, and why it is important for the PDB to report
cell parameters to high precision-
If one calculates a density map, or even R-factor, from your
model and data, it is important to use precisely the same cell
parameters that you refined against, whether they were correct
to that precision or not. Putting your orthogonal-Angstrom
coordinates into a slightly different cell will give different
fractional coordinates and significantly different Fcalc. On
the other hand you can change the parameters by half a percent
and re-refine, and come up with essentially the same statistics
and map. I learned this trying to get a cell that what-check
would be satisfied with, which turned out to be an exercise
in cat-chasing-its-tail (apparently because CNS and whatcheck
have different ideas about ideal bond lengths).
So it depends on what your audience wants to use the information for-
For your journal readers wondering how densely your crystal is
packed or what kind of spot overlap you have, or whether they've
got the same crystal form you solved, 0.1 A is fine.
For someone downloading your coordinates and data to look in the
density to see if there is a post-translational modification you
missed on Tyr 537, give them three-place precision.
Yoder, Marilyn wrote:
Hi all,
I have a reviewer challenging the number of digits to the right of the
decimal point that I have reported in a submitted manuscript. I had
reported 3 digits to the right, frankly because that is what most of the
programs I use report and the PDB coordinate file reports 3 digits to
the right of the decimal in the CRYST1 record. The reviewer doubts that
the value is accurate to that many digits, and suggested reporting to
the tenth of an Angstrom. In corresponding with the PDB, they allow 3
digits to the right of the decimal, but even if one gives the PDB, say
51.1 A as an axis, the CRYST1 record will be padded and will appear as
51.100A.
So my question is .... how does one determine what is a valid accuracy
or precision in unit cell axes? To be honest, I'm not sure what all the
numbers are, and how many significant digits they have, that are used in
calculating unit cell axes.
In my particular case, I have data to 1.73 A, synchrotron radiation,
0.41 degree mosacity. All unit cells are less than 115 A.
