Dear Dale,
For me, a high quality map is a map which clearly shows where the model is correct and where adjustments are needed, e.g. in places where the search model is different from the structure to be solved and in places where the model is missing. This is not the same as a difference in contour level.
The most impressive example I have seen was with proTAFI. Here we had 3 molecules in the asymmetric unit. 2 molecules were well-defined, one was somewhat disordered. The prodomain had 91 residues, the catalytic domain 309. The resolution was 2.5Å (optimistic estimate) and the solvent content was 72%. The structure was solved with phaser using a model of the catalytic domain only (~3/4 of the total). The resulting maps clearly showed positive difference density for the complete 2 well-ordered prodomains (92 residues), which could be fitted in one go. I have never seen something like that with crystals with a lower solvent content (say 50% or less). In these cases we would need several cycles of model building and refinement before the complete missing parts could be fitted.
Best regards,
Herman
-----Original Message-----
From: Dale Tronrud [mailto:[log in to unmask]]
Sent: Tuesday, May 24, 2011 6:33 PM
To: Schreuder, Herman R&D/DE
Cc: [log in to unmask]
Subject: Re: [ccp4bb] how to remove part of data with bad signal to noise ratio
On 5/24/2011 2:35 AM, [log in to unmask] wrote:
> Dear Clement,
>
> In case of a noisy experimental map, you have to do explicit solvent
> flattening. However, in case of molecular replacement, if the model
> occupies only say 30% of the asymmetric unit, the solvent where there
> is no model, will be flattened automatically. You can also view it
> like
> this: if 70% of the asymmetric unit is featureless solvent, the model
> at hand (=flat bulk solvent model), will be very accurate. I never
> really tested this, but in the cases where I had a very high solvent
> content, I was always surprised by the quality of the electron density
> maps. Off
If you choose your contour level based on the map rms (often inappropriately called "sigma") the 2Fo-Fc density of a high-solvent-content map will appear stronger even when the absolute quality is the same. All that flat space will cause the overall rms to be low even if the rms calculated over the protein is the same.
Dale Tronrud
> course, crystals with a high solvent content tend to diffract poorly
> and if the solvent is not featureless, this will not work either.
>
> If you get high Rfree values for a structure with high solvent
> content, I would get suspicious and look for extra molecule(s), which
> may have been overlooked. If these extra molecule(s) are disordered,
> this will off course lead to high Rfree values.
>
> Best,
> Herman
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
> Clement Angkawidjaja
> Sent: Tuesday, May 24, 2011 11:19 AM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] how to remove part of data with bad signal to
> noise ratio
>
> But you have to do solvent flattening (density modification), which
> people often (unintentionally?) skip for structures solved with
> molecular replacement. Please correct me if I am wrong.
>
> Clement
>
> On May 24, 2011, at 6:01 PM, [log in to unmask] wrote:
>
>> This is not my experience. Provided the solvent is featureless, I
>> find
>
>> that a high solvent contents leads to a lower Rfree due to a kind of
>> solvent flattening effect. Of course, if a significant part of the
>> molecule(s) is/are disordered, this will lead to a degradation of the
>> Rfree.
>>
>> My 2 cents,
>> Herman
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