It is true that MAD phasing can give you hyper-accurate phases. This is
because you are measuring the heavy atom signal in both directions on
the Harker diagram, allowing the phase to be solved analytically. The
phasing signal is noisy, of course, but you can fix that either with a
bigger heavy atom (more signal) or by doing a lot of averaging (less
noise). You will probably need more than one crystal.
SAD, on the other hand, can never give you very good phases because the
phase probability distributions are all bimodal. The technology that
makes SAD practical is solvent flattening, but as soon as you start
doing things like solvent flattening you are already imposing a model,
and every model comes with some amount of bias. How important that bias
is depends on the question you are trying to answer.
MIR, like MAD, can get arbitrarily accurate phases, but this and every
other technique requires a high degree of isomorphism.
In practice, essentially all experimental phasing attempts are really
trying to get you just over that ever-elusive tipping point of phase
quality where solvent flattening and model building can take you the
rest of the way. So, in the end what you have are model phases, just
like if you had done MR. It's sad really how fleeting the involvement
of experimental phases are in essentially all MAD/SAD structure
determinations. Pun intended.
That said, model phases are not so bad. In fact, in all my experiments
with fake data the model-phased 2mFo-DFc map always has the best
correlation to the "true" map. If you substitute the "true" phases and
use the 2mFo-DFc coefficients you actually make things worse.
Counter-intuitive, but true.
-James Holton
MAD Scientist
On 12/5/2018 12:07 AM, 香川 亘 wrote:
> Dear all,
>
> It is my understanding that experimental phasing (e.g. Se-SAD), in principle, yields better electron density maps than molecular replacement for protein regions with weak electron densities (partially disordered or flexible). I would appreciate if someone could provide comments on whether my understanding is correct or not. If there any good examples or literatures on this issue I would be grateful to know about it.
>
> I thank you in advance.
>
> Wataru Kagawa
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