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 <[email protected]> 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 <[email protected]> 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 <+61%203%209345%202493> > Email: [email protected] | 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 > > > > ------------------------------ > > 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
