Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Gerard, I was puzzled by the statement that the UCLA anisotropy server characterises anisotropy in terms of a combination of effects restricted to lie along the crystallographic axes. That server is built on the anisotropy correction algorithm in Phaser, and from the beginning Phaser has

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

As others point out, anisotropy is endemic in protein crystals, and severe cases make the single number score for Rmerge, CC1/2 etc pretty meaningless for the outer shell. But do not throw out the meaningful data at your higher resolution because of single number stats- first LOOK at your images

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Khoa Pham, the question of a formal definition of en "effective" resolution and its variability with space direction is discussed in a) Urzhumtseva, L., Klaholz, B.P., Urzhumtsev, A. (2013) " On effective and optical resolution of diffraction data sets". Acta Cryst., D69 , 1921-1934.

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Gerard, Thank you so much for the very interesting discussions and the recommendation of using STARANISO. I will submit my data to STARANISO server and keep you updated. Sincerely, Khoa Pham

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Khoa, You are asking a very pertinent question, that will resonate in (too) many people's minds. Somehow anisotropy is very much "an inconvenient truth" in MX, as many things have long been set up and operated on the basis of having resolution be a single number and of all

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Gerard, Thank you very much for your suggestions. We actually analyzed anisotropy of the data using UCLA-DOE LAB Diffraction Anisotropy Server https://services.mbi.ucla.edu/anisoscale/. The question is that if the data cut in the anisotropically way, should it be deposited to the pdb.

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Khoa, Thank you for your reply and for the news that your data do show strong anisotropy. In such cases, the reflex is indeed to cut the data down to a resolution where the statistics look more reasonable. However, as these statistics are computed in spherical shells, i.e.

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Gerard and James, Thank you very much for the suggestions. My data was collected at APS. Yesterday, an expert in my institution kindly inspected my raw data and pointed out to me that my data are indeed severely anisotropic in the b direction. He also recommended me to cut the data to

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear Khoa, I would lean in the same direction as James, and say that what you need is not advice about what refinement program to use, but a question about whether you could collect better data. With an overall I/sig(I) of 8.3 and an outer-shell value of 0.5, there is just not enough oomph

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

I am not happy with an Rmerge of 20%. Also what is the Rmerge and redundancy in the highest shell, i.e. do you really have the resolution of 2.9? How did you collect this data? SR or lab. James Phillips On Wed, Jun 14, 2017 at 8:09 AM, Khoa Pham wrote: > Dear CCP4

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Dear All, Thank you very much for your suggestions. I will refine the structure and keep you updated. Khoa

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

Hi Khoa, How many rounds of refine and rebuild have you gone through on the graphics? Have you tried Lorestr in CCP4 (Automated refinement of macromolecular structures at low resolution using prior information, Oleg Kovalevskiy, Robert A. Nicholls and Garib N. Murshudov). Ben [At 2.9A

Re: [ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

The R factors may be high because the structure is imperfect - almost inevitable at that resolution - but also there are often serious difficulties with scaling at this resolution . If you are using REFMAC look at the v wrt resolution plot at the end of refinement (follows R and Rfree plot v

[ccp4bb] Antw: Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

If you dont use Phenix, print the figures of https://doi.org/10.1016/S0969-2126(02)00743-8 and use them beside your screen. Helps a lot if you wanna have a quick look at Rfact distributions.. >>> Paul Emsley 14.06.17 15.25 Uhr >>> On 14/06/2017 14:09, Khoa Pham

Re: [ccp4bb] What are acceptable Rwork/Rfree for publication

On 14/06/2017 14:09, Khoa Pham wrote: Dear CCP4 members, I am refining a structure with a resolution of ~ 2.9 A and the Rwork/Rfree are are 0.34/0.37, respectively. My question is that these Rwork/Rfree are acceptable for publication. If you have Phenix, try POLYGON. That will give you a