g by 1 in some direction - did you
> check your direct beam is correct?
>
> and did you check radiation damage actually per frame does the
> diffraction seem to fade out towards the end (if you have high redundancy
> just try with less)?
>
> There is something systematically wrong when you get such a high low res
> Rmerge - i would think - amazing that you can refine it that well…..
>
> if you look at the really low resoution (below its 50-6 in the first
> bin..) what does it look like below 10 Å resolution - also did you try
> XSCALE after XDS and
> crystal_name for correction… at least you can look at low resolution binds
> in more detal if you run it through there… though i am not the specialist
> to talk to
> on what XDS can do for corrections….
>
>
> Best,
> Tommi
>
>
> On 29 Sep 2018, at 10:58, Zhang Foggy > wrote:
>
> 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
>
>
>
>
> Rajesh Kumar 于2018年9月28日周五 下午11:41写道：
>
>> 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 you
>> Rajesh
>>
>> ---x
>> With regards
>> Rajesh K. Harijan, Ph.D.
>> Schramm Laboratory
>> Albert Einstein College of Medicine
>> 1300 Morris Park A
