Guangyu,
If I'm understanding your question correctly; you're asking if all other
things are equal (resolution, degree of disorder, etc), does improving
the data/parameter ratio result in an improved model?
The short answer is: (at least sometimes) yes.
Pete
Guangyu Zhu wrote:
Ian,
Because it is same protein, the high thermal motion is likely caused by crystal
packing, and should be corrected by TLS refinement. The B left over should be
similar.
Anyway, this is just a hypothetical question. I tried to make other things same
and just compare resolution and d/p. But you can still find difference. So if
80% crystal diffract to 3.0A too, then d/p ratio is much higher than 3.0A 50%
crystal, it must be a more accurate refinement. What if 80% crystal diffract to
3.1, 3.2A, or 3.3A? Or I change the question to: could d/p ratio compensate
some resolution?
Thanks!
Guangyu
From: Ian Tickle <[email protected]<mailto:[email protected]>>
Date: Friday, March 15, 2013 6:33 AM
To: System Administrator <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: Re: [ccp4bb] Resolution and data/parameter ratio, which one is more
important?
Hi Guangyu,
I think it's not as straightforward as comparing d/p ratios, that is only one of
several factors that influences precision. Another important factor would be the
overall level of thermal motion & disorder which will most likely be
significantly higher in the 3.6A 80% case; after all that's probably the reason
that it only diffracts to 3.6A!
All things considered I would go for the 3A form.
Cheers
-- Ian
On 15 March 2013 00:27, Guangyu Zhu
<[email protected]<mailto:[email protected]>> wrote:
I have this question. For exmaple, a protein could be crystallized in two
crystal forms. Two crystal form have same space group, and 1 molecule/asymm.
One crystal form diffracts to 3A with 50% solvent; and the other diffracts to
3.6A with 80% solvent. The cell volume of 3.6A crystal must be 5/2=2.5 times
larger because of higher solvent content. If both data collecte to same
completeness (say 100%), 3.6A data actually have higher data/parameter ratio,
5/2/(3.6/3)**3= 1.45 times to 3A data. For refinement, better data/parameter
should give more accurate structure, ie. 3.6A data is better. But higher
resolution should give a better resolved electron density map. So which crystal
form really give a better (more reliable and accurate) protein structure?
