Re: [ccp4bb] correlations of B-factors and resolution
Please not that average B value may be arbitrary depending on data processing program, reference image etc. Average B values could be arbitrary (you can add to all atom single B value and it will not change information content of the data, they are removable). I think either variance of B or - Bmin may correlate with resolution better. regards Garib On 16 May 2012, at 15:06, Nat Echols wrote: > On Wed, May 16, 2012 at 6:46 AM, Qiang Chen wrote: >> 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? > > They're correlated, but it's not an exact relationship. See attached > plot (which includes all entries in the PDB for which structure > factors were deposited, as of about a year ago). The mean B-factor > for structures between 2.3A and 2.5A resolution is just under 40, so > your structure is very reasonable (the distribution is quite wide). > >> 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? > > Only to the extent that high solvent content tends to result in more > poorly ordered crystals and worse resolution - also, perhaps surface > side chains will be more flexible if they're not forming crystal > contacts. But it doesn't inherently change anything in refinement, > aside from making it easier because you have a better > observations-to-parameters ration. > > -Nat > Dr Garib N Murshudov Group Leader, MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
Re: [ccp4bb] correlations of B-factors and resolution
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: t...@shelx.uni-ac.gwdg.de >> Subject: Re: [ccp4bb] correlations of B-factors and resolution >> To: CCP4BB@JISCMAIL.AC.UK >> >> -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- >
Re: [ccp4bb] correlations of B-factors and resolution
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: t...@shelx.uni-ac.gwdg.de > Subject: Re: [ccp4bb] correlations of B-factors and resolution > To: CCP4BB@JISCMAIL.AC.UK > > -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-
Re: [ccp4bb] correlations of B-factors and resolution
-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-
[ccp4bb] correlations of B-factors and resolution
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.
