Re: [ccp4bb] PDB Submission of SAD data.

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

Previous message:
Subject: Re: two identical proteins in one asymmetric unit
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-03-24

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From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
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Subject: Re: PDB Submission of SAD data.
From: Huanwang Yang hyang {- at -} RCSB {- dot -} RUTGERS {- dot -} EDU
Date: 2009-03-24

Dear Francis
You do not have to tell which columns were used for refinement. The
program should pick FP/SIGFP. You can deposit the foo.mmcif and your
coordinate to the PDB.
The alternative to convert/validate your mtz file is to use the server
http://pdb-extract.rcsb.org/auto-check/ . It is easy to use. Also the
web page is updated faster than the standard alone program.

Regards,
Huanwang

Francis E Reyes wrote:
> I have a mtz from Autosol/resolve that has the following columns:
> OVERALL FILE STATISTICS for resolution range 0.002 - 0.261
> =======================
>
>
> Col Sort Min Max Num % Mean Mean Resolution
> Type Column
> num order Missing complete abs. Low
> High label
>
> 1 ASC 0 37 0 100.00 18.7 18.7 23.68
> 1.96 H H
> 2 NONE 0 25 0 100.00 7.3 7.3 23.68
> 1.96 H K
> 3 NONE 0 58 0 100.00 20.5 20.5 23.68
> 1.96 H L
> 4 NONE 2.3 316.2 0 100.00 20.39 20.39 23.68
> 1.96 F FP
> 5 NONE 0.1 17.2 0 100.00 1.77 1.77 23.68
> 1.96 Q SIGFP
> 6 NONE -180.0 180.0 0 100.00 6.24 89.14 23.68
> 1.96 P PHIM
> 7 NONE 0.000 0.998 0 100.00 0.283 0.283 23.68
> 1.96 W FOMM
> 8 NONE -10.9 11.8 0 100.00 0.01 0.46 23.68
> 1.96 A HLAM
> 9 NONE -10.7 20.6 0 100.00 0.00 0.46 23.68
> 1.96 A HLBM
> 10 NONE -4.1 4.5 0 100.00 -0.00 0.08 23.68
> 1.96 A HLCM
> 11 NONE -3.5 3.1 0 100.00 0.00 0.07 23.68
> 1.96 A HLDM
> 12 NONE 0.0 1.0 0 100.00 0.10 0.10 23.68
> 1.96 I FreeR_flag
> 13 BOTH 0.0 0.0 0 100.00 0.00 0.00 23.68
> 1.96 F FC
>
>
> Should I just prepare my mmcif by pdb_extract_sf -dt F -dp MTZ -c 1 -w
> 1 -iDAT exptl_fobs_phases_freeR_flags.mtz -o foo.mmcif and submit
> foo.mmcif to the PDB?
> Do i need to separately indicate which columns (in my case FP/SIGFP)
> were used for refinement?
>
> Thanks
>
> FR
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Huanwang Yang Ph.D. *
* RCSB Protein Data Bank *
* Dep. of Chemistry & Chemical Biology, Rutgers University *
* 610 Taylor Road, Piscataway, NJ 08854-8087 *
* Phone: (732)-445-0103 (ext 240); Fax: (732)-445-4320 *
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

CCP4bb navigation

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

Previous message:
Subject: Re: two identical proteins in one asymmetric unit
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2009-03-24

Next message:
Subject: Re: OT: Crystallisation compatible detergents
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2009-03-24