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CCP4BB  August 2007

CCP4BB August 2007

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Subject:

The importance of USING our validation tools

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Wed, 15 Aug 2007 15:11:10 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (74 lines) , 60_truncate.log (1039 lines) , 62_refmac5.log (964 lines) , 63_baverage.log (2448 lines)

 There is a correspondence in last weeks Nature commenting on the 
disparities between  three C3B structures. These are:
 2icf   solved at 4.0A resolution, 2i07 at 4.1A resolution, and 2hr0 at 
2.26A resolution.

 The A chains of all 3 structures agree closely, with each other and 
other deposited structures.
 The B chains of 2icf and 2i07 are in reasonable agreement, but there 
are enormous differences to the B chain of 2hr0.
 This structure is surprisingly out of step, and by many criteria likely 
to be wrong.

 There has been many articles written on validation and it seems worth 
reminding crystallographers
of  some of tests which make 2hr0 suspect.

1) The cell content analysis suggests there is 80% solvent in the 
asymmetric unit.
 Such crystals have been observed but they rarely diffract to 2.26A.

2) Data Analysis:
 The reflection data has been deposited so it can be analysed.
 The plots provided by TRUNCATE showing intensity statistic features are 
not compatible with such a high solvent ratio.   They are too perfect; 
the moments are perfectly linear, unlikely with such large volumes of 
the crystal containing solvent, and there is absolutely no evidence of 
anisotropy, again unlikely with high solvent content.

3)  Structure analysis
 a) The Ramachandran plot is very poor ( 84% allowed) with many residues 
in disallowed regions.
 b) The distribution of residue B values is quite unrealistic. There is 
a very low spread,  which is most unusual for a structure with long 
stretches of exposed chain.  The baverage log file is attached.

 c) There does not seem to be enough contacts to maintain the 
crystalline state.

The only symmetry contacts found by distang are:
 T   92 CG2  A   N 1641 CB   B      2.695 -X,Y,-Z                 1.00   
28.50
 T   92 CG2  A   N 1641 OD1  B      2.813 -X,Y,-Z                 1.00   
30.70
 E  731 OE1  B   D  944 OD1  B      2.641 -X+1/2,Y+1/2,-Z [0-1 0] 1.00   
30.94

The MSDpisa site reports:
Buried surface between A & B 4117 A**2
Crystal generated surfaces: B to B'   277A**2  and B to B"  144A**2.

 4) Map analysis.
  I ran the structure through REFMAC to generate weighted maps.
  The R factor and FreeR are unreasonably close  I think.  0.179   0.194 
out of REFMAC.
  They also show a very unusual profile; lowest in the lowest resoultion 
shell.
  The plots of <Fobs> v <Fc> as a function of resolution overlap almost 
perfectly.

  And the maps (displayed in COOT)  are very strange - there are many 
10-20 Sigma peaks in the difference map, and these can be explained by 
quite simple re-adjustments of the coordinates. I suspect that the 
"observed amplitudes" which are available are  in fact calculated from a 
closely related structure.


 I attach the baverage, truncate and refmac log files so that interested 
readers can look at these  log graphs.

 Eleanor Dodson
 


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