Hello Yarrow,
Since you have a refined molecular replacement solution I recommend
using that rather than global intensity statistics.
Obviously if you solve in P21 and it's really P212121 you should have
twice the number of molecules in the asymmetric unit and one half of the
P21 asymmetric unit should be identical to the other half.
Since you've got decent resolution I think you can determine the real
situation for yourself: one approach would be to test to see if you can
symmetrize the P21 asymmetric unit so that the two halves are identical.
You could do this via stiff NCS restraints (cartesian would be better
than dihedral). After all the relative XYZs and even B-factors would be
more or less identical if you've rescaled a P212121 crystal form in P21.
If something violates the NCS than it can't really be P212121.
Alternatively you can look for clear/obvious symmetry breaking between
the two halves: different side-chain rotamers for surface side-chains
for example. If you've got an ordered, systematic, difference in
electron density between the two halves of the asymmetric unit in P21
then that's a basis for describing it as P21 rather than P212121.
However if the two halves look nearly identical, down to equivalent
water molecule densities, then you've got no experimental evidence that
P21 with 2x molecules generates a better model than P212121 than 1x
molecules. An averaging program would show very high correlation
between the two halves of the P21 asymmetric unit if it was really
P212121 and you could overlap the maps corresponding to the different
monomers using those programs.
Phil Jeffrey
Princeton
