Dear All,
Thanks to everyone who contributed with remarks and suggestions, I do
appreciate the advice. I ought to have mentioned in the earlier post that data
resolution limits were based on CC1/2, I/sigma and Rmeas cut-offs and that
Zanadu (CCP4 program) had concluded that the assignment of P2(1) seemed to be
correct based on refinement R-factors in the different subgroups (P1 and P2(1)).
Since the maps in P2(1) look great with well-defined density for bound ligands
and areas of interest, I am going with Eleanor's suggestion (please see below).
Some of you have pointed out that an Rfree of 28% is not too bad for a tNCS
problem, which gives me hope that the reviewers will not frown at the structure
stats.
Below is an abbreviated summary of the responses received.
Mark J van Raaij and Robyn Stanfield: Space group or origin ambiguities due to
pseudo-symmetry may be resolved using the program Zanadu (CCP4).
Oleg Tsodikov: Check for signs of radiation damage in scaling statistics
because of higher R/Rfree in P1. Oleg also said that scaling statistics are not
always easily interpretable by eye in case of tNCS.
Randy Read said that one cannot assume a crystal is twinned if the L-test and
the Phaser second moments test (after tNCS correction) do not support the
conclusion. He pointed out that tests using potential twin laws are based on
the assumption that twin-related reflections should have independent
intensities, which is not true *either* when there is twinning *or* when the
data have been merged in too low symmetry.
! I did have this problem, i.e., 'false' twinning arising due to data
processed in far lower symmetry (P1).
Eleanor Dodson said that Rfactors are higher for data sets with strong pseudo
translation as it forces a subset of the reflections to be systematically weak
and weak reflections always have higher R factors. She also warned about false
twinning and concluded that if the maps look good, one can be happy with the
results.
Many thanks again,
Renu
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Renu Kadirvelraj
Assistant Research Scientist
Biochemistry and Molecular Biology
120, Green Street
University of Georgia
Athens, GA 30605
Tel: (706) 583 0303
[email protected]
