My first check would be to inspect the data processing plots -
Wilson Plot? Is it normal? predicted B factor of 8 - why?

Then the plot from  refmac <Fo> and <Fc> v resolution?
Is there a scaling abnormality?

B of 8 is surprisingly low for that resolution  but maybe the crystals just did not have enough oomph to go to their limit..

Eleanor




On Mon, 4 Nov 2019 at 07:00, Anastassis Perrakis <[log in to unmask]> wrote:
Dear Michael,

Exactly because the B factor is only 8, the intensity as function of resolution is droping really slowly, and thus the I/sigI 4.7 at low resolution drops so slowly to 1.0.

I would almost bet you have a low solvent content.

The data are fine imo.

Best,

Tassos

On Nov 4, 2019, at 0:18, Michael Jarva <[log in to unmask]> 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
The ACRF Chemical Biology Division is supported by the
Australian Cancer Research Foundation

_______________________________________________ 

The information in this email is confidential and intended solely for the addressee.
You must not disclose, forward, print or use it without the permission of the sender.

The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the Kulin 
Nation as the traditional owners of the land where our campuses are located and 
the continuing connection to country and community.
_______________________________________________

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1


To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1