[ccp4bb] Amazing B-factor

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 3D LCD and glasses
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2009-06-01

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Subject: Re: 3D LCD and glasses
From: Stuart McNicholas mcnicholas {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-06-01

Subject: Amazing B-factor
From: Jian Wu protease {- at -} GMAIL {- dot -} COM
Date: 2009-06-01

Dear all,

Recently we have collected one set of data which is processed to 2.9A and
3.0A and the Wilson-B values are 50.1 and 59.1, respectively. As for the
completeness of the highest shell is only 66% in 2.9A (80% in 3.0A), we use
the dataset with 3.0A for phasing and refinement.

Everything is OK during phasing. Routinely, we use CNS (rigid, minimize and
bgroup) for primary refinement and the R and freeR values go to 31.1 and
34.1. Surprisingly, the B-factor is 137.2. I have modified the B-factor to a
fixed value (59.1 A^2) in the searching model coordinate file, however it
changed to 127.6 after 'rigid' and subsequently to 131.9 after 'minimize'.
In all the scripts above I used the default option "anisotrpic" at "overall
B-factor correction". I don't know whether it is right to use this option at
low resolution, so I have tried the other two options "no" and "isotropic".
In the 1st choice, the B-factor is seemingly reasonable (55~59) but the R
and freeR are very high (45.9 and 51.9). In the 2nd choice, the B-factor, R
and freeR values are between those of the other two options (111.3, 40.6,
and 45.3). I want to know what cause these surprising changes especially for
B-factor value.

Any suggestion is appreciated.

Jian Wu

--
Jian Wu

Ph.D. Student
Institute of Biochemistry and Cell Biology
Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences (CAS)
Tel: 0086-21-54921117
Email: protease@gmail.com

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: 3D LCD and glasses
From: Warren DeLano warren {- at -} DELSCI {- dot -} COM
Date: 2009-06-01

Next message:
Subject: Re: 3D LCD and glasses
From: Stuart McNicholas mcnicholas {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-06-01