JISCMail - CCP4BB Archives

[log in to unmask]">

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: [log in to unmask] | Web: http://www.wehi.edu.au/

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