Hi Tongqing,
apart from potential space group related issues that the other mentioned
already, I can't really see anything wrong.
Here is how your R-factors compare to the other R-factors for all
similar structures in PDB:
Histogram of Rwork for models in PDB at resolution 2.50-2.70 A:
0.137 - 0.161 : 20
0.161 - 0.185 : 143
0.185 - 0.209 : 469
0.209 - 0.233 : 624
0.233 - 0.258 : 317
0.258 - 0.282 : 65 <<<< your model
0.282 - 0.306 : 10
0.306 - 0.330 : 2
0.330 - 0.354 : 0
0.354 - 0.378 : 1
Histogram of Rfree for models in PDB at resolution 2.50-2.70 A:
0.190 - 0.217 : 54
0.217 - 0.245 : 281
0.245 - 0.273 : 602
0.273 - 0.300 : 582
0.300 - 0.328 : 104
0.328 - 0.355 : 21 <<<< your model
0.355 - 0.383 : 6
0.383 - 0.410 : 0
0.410 - 0.438 : 0
0.438 - 0.465 : 1
Histogram of Rfree-Rwork for all model in PDB at resolution 2.50-2.70 A:
0.002 - 0.012 : 17
0.012 - 0.022 : 67
0.022 - 0.031 : 164
0.031 - 0.041 : 312
0.041 - 0.051 : 283
0.051 - 0.061 : 344
0.061 - 0.071 : 240
0.071 - 0.080 : 139 <<< your model
0.080 - 0.090 : 55
0.090 - 0.100 : 30
Number of structures considered: 1651
You can try to tun it through AutoBuild in PHENIX in hope that it will
rebuild it and may be improve.
Pavel.
On 6/15/10 7:09 AM, Zhou, Tongqing (NIH/VRC) [E] wrote:
Pavel,
Thanks for looking into this. Attached are the data and pdb files. I
run xtriage, it reported some data problem saying my symmetry is low,
should be P422 instead of P222, but HKL2000 indexing won't even pickup
tetragonal SG. When we were collecting data, we noticed the
diffraction in a specific rotation orientation was very mosaic, seem
like a secondary crystal, but HKL2000 managed picking up the right
spots.
Just to add into this, another crystal in the same condition indexed
as P222, but b axis was doubled. That data set could not be refined
further either.
Don't spend too much time on this, I will have APS beam time on
Friday, so I may just fly there to get another data set.
Thank you again,
Tongqing
*Tongqing Zhou, Ph.D. *
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
*/******************************************************************/*//
*/The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient. If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices. National Institute of
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of the NIAID by one of its representatives./*
*/******************************************************************/*
*From:* Pavel Afonine [mailto:[email protected]]
*Sent:* Tuesday, June 15, 2010 1:16 AM
*To:* Zhou, Tongqing (NIH/VRC) [E]
*Subject:* Re: [ccp4bb] Stuck refinement
Hi,
if you send me the data and model then I will have a look. I have some
hypotheses about why this is happening but before I say something I
would like to hava a look at the data.
Pavel.
On 6/14/10 1:57 PM, Zhou, Tongqing (NIH/VRC) [E] wrote:
Hi Everyone,
I have some problem in refining a structure. The data goes to 2.4A
(with some 30% completeness at 2.15A), the structure was solved by MR
with Phaser, refinement was done with Phenix, but the r and r-free are
now staying at 26% and 32%, even with all possible waters and missing
fragments added. Data was collected at APS at cryo condition. One
thing I noticed during HKL2000 data processing was that the chi^2 were
way too high at lower resolutions shells, I had to adjust the default
error model in HKL2000 to get the chi^2 to around 1, but this
adjustment reduced the overall I/sigI ratio a lot (from around 20 to 5).
The quality of electron density maps looks fine to me for a 2.4 A data
set and I was able to build all the missing CDR loops for the antibody
in the complex. I am lost now, should I just re-collect a new data set?
Thanks,
Tongqing
*Tongqing Zhou, Ph.D. *
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
*/******************************************************************/*
*/The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient. If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices. National Institute of
Allergy and Infectious Diseases shall not accept liability for any
statements made that are sender's own and not expressly made on behalf
of the NIAID by one of its representatives./*
*/******************************************************************/*
On 6/14/10 1:57 PM, Zhou, Tongqing (NIH/VRC) [E] wrote:
Hi Everyone,
I have some problem in refining a structure. The data goes to 2.4A
(with some 30% completeness at 2.15A), the structure was solved by MR
with Phaser, refinement was done with Phenix, but the r and r-free are
now staying at 26% and 32%, even with all possible waters and missing
fragments added. Data was collected at APS at cryo condition. One
thing I noticed during HKL2000 data processing was that the chi^2 were
way too high at lower resolutions shells, I had to adjust the default
error model in HKL2000 to get the chi^2 to around 1, but this
adjustment reduced the overall I/sigI ratio a lot (from around 20 to 5).
The quality of electron density maps looks fine to me for a 2.4 A data
set and I was able to build all the missing CDR loops for the antibody
in the complex. I am lost now, should I just re-collect a new data set?
Thanks,
Tongqing
*Tongqing Zhou, Ph.D. *
Staff Scientist
Structural Biology Section
Vaccine Research Center, NIAID/NIH
Building 40, Room 4607B
40 Convent Drive, MSC3027
Bethesda, MD 20892
(301) 594-8710 (Tel)
(301) 793-0794 (Cell)
(301) 480-2658 (Fax)
*/******************************************************************/*//
*/The information in this e-mail and any of its attachments is
confidential and may contain sensitive information. It should not be
used by anyone who is not the original intended recipient. If you have
received this e-mail in error please inform the sender and delete it
from your mailbox or any other storage devices. National Institute of
Allergy and Infectious Diseases shall not accept liability for any
statements made that are sender's own and not expressly made on behalf
of the NIAID by one of its representatives./*
*/******************************************************************/*
