[log in to unmask]">Dear All,
Thanks for your kindly comments. Here are the summary and my responses:
1.Summary:
The high value of the R-merge might be due to the weak diffraction, as well as the collection method (low dose per image and high redundancy).The suggetions is ignore the R-merge value, and condider the Rpim, CC1/2 and I/sigI value instead.
2. Responses to the comments:
(1) Dr. Herman Schreuder suggested that I can use ADXV to look through my data and see if there is some bad regions, overload (scale only the first 30-40 frames) or ice rings, and I also can use other software to scale the data (xds, mosfilm etc.)Response: Actually I have tried these alternative ways. Indeed, the diffraction of my crystals is pretty good (you can see the image from attached jpg file), there is no ice rings, no significant radiation damage, no bad regions through the entire frames. I have also tried to use xds to scale it, unfortunately, the R-merge is still high (~50%). Additionally, I also tried to only scale part of the frames, however, the R--merge is to ~48%.
(2) Dr. Shepard William suggested to try mosfilm or xds, and asked the multiplicity of the data.Response: I have tried to scale with XDS, but there is no improvement. The space group is P43. I can refine the structure to R-value 0.19, R-free 0.23, indicating that the space group should be correct. I have also tried to scale to P21 or P1, and there is no improve in R-merge.
(3) Dr. Phil Evans mentioned that Rmerge is a terrible criterion (Science, 2012, 336,1030), and CC(1/2) should be generally considered as the best criterion. In my case, both of the Rmerge (1.59) and CC(1/2) (0.645) in the outer shell are acceptable. However, the Rmerge (0.284) and CC(1/2) (0.975) in the inner shell looks not perfect. I should consider the radiation damage.Response: Thanks a lot for the comments. As you can see from the attached figure, the diffraction is sharp, and I do not see any significant radiation damage
(4) Dr. Ditlev Egeskov Brodersen suggested to double check the space group and process part of the data.Response: as I mentioned in (1) and (2), I have tried to only scale part of the frames, however, the R--merge is to ~48%; I can refine the structure to R-value 0.19, R-free 0.23 under the current space group P43. Moreover, scale to P21 or P1,can not improve the R-merge significantly.
(5) Dr. Remy Loris mentioned that a high value of R-merge indicates a wrong symmetry or very weak data. from my data, the reason could be the weak data as well as high redundancy.Response: I agree. from the attached image, I can see the the diffraction is sharp but weak. However, increse the exposure time will introduce more radiation damage....
(6) Dr. Edward A. Berry mentioned that my data has rather high redundancy as Rpim is much lower than Rmeas value. It could be caused by collecting low dose per image and making up for it with high redundancy, Dr. Edward A. Berry suggeted to Look instead at CC1/2 and I/sigI which seem fine.Response: Thanks for the comments, and I agree.
(7). Dr. Rajesh Kumar raj suggested me to consider Rpim, CC1/2 and I/sigI for cutting the data as Rmerge is old approach and it is data redundancy dependent.
Thank you for your kindly help again!
Best,
Liang
I totally agree with Berry. Please consider Rpim, CC1/2 and I/sigI for cutting the data. Rmerge is old approach as it is data redundancy dependent.
Thank youRajesh
---xxxxx----With regardsRajesh K. Harijan, Ph.D.Schramm LaboratoryAlbert Einstein College of Medicine1300 Morris Park Ave., Bronx, NY 10461Tel: 718.430.2777 | Fax: 718.430.8565
The fact that chi^2 is approximately 1.0 in all shells says that the deviations are about what is expected from the error model. The fact that Rpim is much lower than Rmeas means that you have rather high redundancy. This would seem to be a case of collecting low dose per image and making up for it with high redundancy, a strategy that has been recommended to ensure a full dataset even in the case of high radiation sensitivity. In my opinion the high Rmerge is nothing to worry about. Look instead at CC1/2 and I/sigI which seem fine.
On 09/28/2018 04:09 AM, Zhang Foggy wrote:
> Dear All,
>
> Sorry for the off-topic.
>
> I recently collected a set of data. The diffraction spots are extremely sharp. However, When I used HKL3000 to scale it, I get a final resolution at 3.1A with overall R-merge ~0.54 (R-merge in the highest 3.2A-3.1A shell: 1.59). Then I solve the structure with final R value 0.19 and R free value 0.24 although I know this Rmerge value is totally unacceptable, and the density looks perfect.
>
> I also tried to collect other four set of data with different crystals. unfortunately, all of them have same problem.
>
> I ask one of my friend who is an expert in HKL3000, but he had no idea about it. Does anyone has suggestions?
>
> Here is the scale information for your review:
> Space group: P43 (I also tried P1, the Rmerge value is still similar)
>
> Shell Lower Upper Average Average Norm. Linear Square
> limit Angstrom I error stat. Chi**2 R-fac R-fac Rmeas Rpim CC1/2 CC*
> 50.00 6.67 11.6 0.9 0.3 1.165 0.191 0.284 0.198 0.052 0.975 0.994
> 6.67 5.30 4.5 0.5 0.3 0.952 0.317 0.313 0.329 0.086 0.971 0.993
> 5.30 4.63 7.3 0.7 0.5 0.961 0.293 0.297 0.304 0.081 0.975 0.994
> 4.63 4.21 7.0 0.8 0.6 0.986 0.369 0.358 0.382 0.101 0.969 0.992
> 4.21 3.91 5.6 0.8 0.6 1.040 0.522 0.491 0.541 0.142 0.955 0.988
> 3.91 3.68 4.6 0.9 0.7 1.064 0.718 0.669 0.746 0.203 0.929 0.981
> 3.68 3.49 3.5 0.9 0.8 1.092 1.059 0.986 1.101 0.299 0.882 0.968
> 3.49 3.34 2.6 0.9 0.8 1.092 1.382 1.298 1.438 0.395 0.829 0.952
> 3.34 3.21 2.1 0.9 0.8 1.084 1.543 1.489 1.614 0.468 0.772 0.933
> 3.21 3.10 1.6 0.9 0.8 1.070 1.591 1.669 1.680 0.529 0.645 0.885
> All reflections 5.0 0.8 0.6 1.048 0.538 0.487 0.559 0.153
>
> Thank you.
>
> Liang
>
>
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