Re: [ccp4bb] PDB Validation Report

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

Previous message:
Subject: refmac problem
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-01-05

Next message:
Subject: Judging a homology model
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2010-01-05

Subject: Re: PDB Validation Report
From: Jasmine Young jasmin {- at -} RCSB {- dot -} RUTGERS {- dot -} EDU
Date: 2010-01-05

Dear Katja,

You can find below information from PDB Format Guide,
http://www.wwpdb.org/documentation/format32/remarks2.html#REMARK%20500.
The improper CA-C-CB-N angles for chiral centers are calculated and are
listed in REMARK 500 of PDB file.
It is defined below with 10 degree allowed deviations.

+35 for L amino acids
-35 for D amino acids

* +25 to +45 degree range is defined as sp3, L.
If D is expected, it gives "WRONG HAND" in the details. If the
calculated value is positive and outside this range, it gives "OUTSIDE
RANGE" in the details.
* -10 to +10 degree range is defined as sp2, planar.
If it is expected to be sp2 and the value is outside this range, it
gives "EXPECTING PLANAR" in the details. If it is expected to be sp3 and
the value is within this range, it gives "EXPECTING SP3" in the details.
* -45 to -25 degree range is defined as sp3, D.
If L is expected, it gives "WRONG HAND" in the details. If the
calculated value is negative and outside this range, it gives "OUTSIDE
RANGE" in the details.

Hope this information help.

Jasmine

> From: Katja Schleider
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] PDB Validation Report
>
> Dear all,
>
> I just finished my first protein structure. More or less. I'm using
> right now the pdb
> validation server to check the data and the data look quite well. The
> only point
> irretating is following line in the Adit Validation Report:
>
> The following residues have unexpected configuration of the
> chiral center using C(i) - N(i) - Ca(i) - Cb(i) chirality.
>
> Residue Chain Sequence Improper Details
> LYS A 470 22.18 Expecting L Found L OUTSIDE RANGE
> I am not sure what this means and what I should do. What is outside
> the L range? I would be thankful for any advice.
>
> Thanks,
>
> Katja
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

--
===========================================================
Jasmine Young, Ph.D.
RCSB Protein Data Bank
Assistant Research Professor
Lead biocurator
Department of Chemistry and Chemical Biology
Rutgers The State University of New Jersey
610 Taylor Road
Piscataway, NJ 08854-8087

Email:+jasmin@rcsb.rutgers.edu
Phone:+(732)445-0103+ext 231 Fax: (732)445-4320
===========================================================

CCP4bb navigation

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

Previous message:
Subject: refmac problem
From: Jane Bailey jbailey {- dot -} xtal {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-01-05

Next message:
Subject: Judging a homology model
From: Raja Dey deyraja1 {- at -} YAHOO {- dot -} CO {- dot -} IN
Date: 2010-01-05