Dear Michael The Rmerge in the strong intensity bin of 0.079 is untypically high it seems to me. Were the diffraction images underexposed? Best wishes John
Emeritus Professor of Chemistry John R Helliwell DSc_Physics > On 3 Nov 2019, at 23:19, 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 > 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
