Hi,

Thanks for all the suggestions and comments! I have 1635
reflections(5.0%)for the test set. PDB_REDO gives lower R and Rfree. Shall
I refine it further and re-deposit it?

Thanks!

> Hi Tim,
>
> With small test sets, R-free doesn't become meaningless you just have to
> take into account that R-free has an error margin which is higher than for
> cases with a large test set.
> Few people report this error margin, but with a small data set you can
> easily do K-fold cross validation. I.e. do K refinements with K = 1/(test
> set fraction) and report R and R-free as averages with a standard
> deviation (instead of what we call cross validation, but is actually
> holdout validation). The CCP4 program freerflag already splits your data
> set in K groups to make it easier for the user.
> I do this automatically in PDB_REDO if the test set contains fewer than
> 500 reflections. It's amazing how much R-free is influenced by the choice
> of ones test set.
>
> Cheers,
> Robbie
>
>> Date: Wed, 16 May 2012 16:06:24 +0200
>> From: [log in to unmask]
>> Subject: Re: [ccp4bb] correlations of B-factors and resolution
>> To: [log in to unmask]
>>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> Dear Qiang,
>>
>> without much explanation, rather from experience, the average B-factor
>> rises as resolution drops. It does make sense in a way because high
>> B-factors indicate some degree of disorder and disorder is usually the
>> cause for the resolution limit. 48A^2 for a 2.4A structure sound
>> perfectly fine with me, I would not worry provided that all other
>> statistices seem sound.
>>
>> High solvent content surely affects the B-values. The larger the
>> solvent channels and smaller the contact area between the molecules,
>> the more likely they become less stable and less ordered.
>>
>> R and Rfree seem also very good, although the gap is relatively tight.
>> Did you make sure your Rfree set contains at least 500 reflections?
>> The default of 5% often used, can lead to fewer reflections than 500
>> at medium or low resolution, and with less than 500 reflection Rfree
>> becomes statistically meaningless - at least according to Axel
>> Brunger's article about that topic.
>>
>> Cheers,
>> Tim
>>
>> On 05/16/12 15:46, Qiang Chen wrote:
>> > Dear all,
>> >
>> > I have a 2.4A structure(pdb code 3LAF)with an average protein
>> > b-factor of 48. I wonder whether it's acceptable. Is there a direct
>> > correlation of b-factor and resolution? The R and Rfree are 21.1%
>> > and 23.1%, respectively. This structure has a very high solvent
>> > content, 75%. Does it affect the b-factors?
>> >
>> > Thanks a lot!
>> >
>> > Qiang
>> >
>> >
>> > The information in this e-mail is intended only for the person to
>> > whom it is addressed. If you believe this e-mail was sent to you in
>> > error and the e-mail contains patient information, please contact
>> > the Partners Compliance HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was sent to
>> > you in error but does not contain patient information, please
>> > contact the sender and properly dispose of the e-mail.
>> >
>>
>> - --
>> - --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>>
>> GPG Key ID = A46BEE1A
>>
>> -----BEGIN PGP SIGNATURE-----
>> Version: GnuPG v1.4.12 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>>
>> iD8DBQFPs7RgUxlJ7aRr7hoRAnS8AJ472kwIWxf7rqDOhEPSBG5ipvQOWQCeNHNk
>> bum4yGTB56Wtt0JbkixleCw=
>> =uIfE
>> -----END PGP SIGNATURE-----
>