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: [email protected] >> Subject: Re: [ccp4bb] correlations of B-factors and resolution >> To: [email protected] >> >> -----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----- >
