Re: [ccp4bb] Unusual dataset with high Rmerge and extremely low b-factors?

Sun, 03 Nov 2019 18:26:59 -0800

Given that the I/sigma(I) is quite low the high R-merge values are probably to be expected. If the data were stronger, an R-merge that high would indicate that the space group was wrong or the data misindexed. If the multiplicity was higher you could process the data in lower symmetry space group (P1) and see if the R-merge became appreciably lower, but I'm not sure that it will be sensible to do that with such a low multiplicity, still it's probably worth doing. I think if you explain the vagaries of the crystals and data when you publish and/or deposit, I think it should be OK with the referees, especially if the map looks good. I would not worry too much about the mean B-factor but it might be interesting to see the Wilson plot.

On 3 Nov 2019 23:18, Michael Jarva <jarv...@wehi.edu.au> wrote:
Hi CCP4BB,

I have some unusual crystal diffraction data I'd like to get your input on.

Almost a year ago I shot some small rods sticking out of a loop, so basically no liquid around them - using the microfocus MX2 beamline at the australian synchrotron, collected on an EIGER 16M detector.

The crystals diffracted weakly and was seemingly not viable at first glance because of high Rmerge/Rpims. See the aimless summary at the bottom of this post. This seemed to stem from a low spot intensity at low resolutions (I/sd(I)=4.6), but since the CC1/2 was fine I went with it anyway.

Here I also noted an unusually low Mosaicity, 0.05, and Wilson B-factors, 8.02 Å^2.

Density maps looked great and the build refined easily enough (R/Rfree 0.1939/0.2259) with a mean B-factor of 19.85, which according to phenix is lower than any other structure deposited in that resolution bin. Furthermore, the molprobity score is 0.83, and overall real-space correlation CC is 0.855.

So my question is, can I feel comfortable depositing this? 

best regards
Michael

Chosen Solution:    space group P 1 21 1
Unit cell:    44.93   41.90   45.83      90.00  115.57   90.00
Number of batches in file:   1659
The data do not appear to be twinned, from the L-test
Overall InnerShell OuterShell

Low resolution limit                       41.34     41.34      2.49
High resolution limit                       2.40      8.98      2.40

Rmerge  (within I+/I-)                     0.231     0.084     0.782
Rmerge  (all I+ and I-)                    0.266     0.099     0.983
Rmeas (within I+/I-)                       0.323     0.118     1.091
Rmeas (all I+ & I-)                        0.317     0.118     1.167
Rpim (within I+/I-)                        0.225     0.084     0.759
Rpim (all I+ & I-)                         0.171     0.063     0.623
Rmerge in top intensity bin                0.079        -         - 
Total number of observations               19901       362      2067
Total number unique                         6054       126       611
Mean((I)/sd(I))                              2.7       4.6       1.0
Mn(I) half-set correlation CC(1/2)         0.958     0.991     0.570
Completeness                                98.6      98.2      97.3
Multiplicity                                 3.3       2.9       3.4
Mean(Chi^2)                                 0.48      0.33      0.50

Anomalous completeness                      81.7      92.2      75.1
Anomalous multiplicity                       1.5       1.8       1.9
DelAnom correlation between half-sets     -0.003     0.041     0.045
Mid-Slope of Anom Normal Probability       0.704       -         -  

The anomalous signal appears to be weak so anomalous flag was left OFF

Estimates of resolution limits: overall
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50:                         limit =  2.67A 
   from Mn(I/sd) >  2.00:                         limit =  2.87A 

Estimates of resolution limits in reciprocal lattice directions:
  Along    0.96 a* - 0.28 c*
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50:                         limit =  2.40A  == maximum resolution
  Along k axis
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50:                         limit =  2.86A 
  Along   -0.17 a* + 0.99 c*
   from half-dataset correlation CC(1/2) >  0.30: limit =  2.40A  == maximum resolution
   from Mn(I/sd) >  1.50:                         limit =  2.98A 

Anisotropic deltaB (i.e. range of principal components), A^2:  8.62

Average unit cell:    44.93   41.90   45.83   90.00  115.57   90.00
Space group: P 1 21 1
Average mosaicity:   0.05

Minimum and maximum SD correction factors: Fulls   1.27   1.28 Partials   0.00   0.00




Michael Jarva, PhD
ACRF Chemical Biology Division

The Walter and Eliza Hall Institute of Medical Research
1G Royal Parade
Parkville Victoria 3052
Australia

Phone: +61 3 9345 2493 
Email: jarv...@wehi.edu.au | Web: http://www.wehi.edu.au/

The ACRF Chemical Biology Division is supported by the

Australian Cancer Research Foundation


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