Here are some solved models information (no P 21): 1: 56.69, 75.87, 74.927; 90, 91.857, 90; P1 21 1; 4 copies in asynmm unit. 2: 46.732, 32.276, 51.065; 90, 94.372, 90; P 1 21 1; 1 copy in ASU. 3. 115.631, 115.631, 101.828; 90, 90, 90; I 41; 2 copies in ASU.
The estimated molecules in my new form is 4 copies in ASU. Thanks, Shen On Mon, Nov 11, 2019 at 11:06 AM Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > Hmm - > cell dimension of your solved model? Number of molecules in the P21 > crystal? > > Likely number of molecules in asymm unit for your new form? > > Eleanor > > > > On Mon, 11 Nov 2019 at 15:51, Xu, Shenyuan <x...@miamioh.edu> wrote: > >> Hello Eleanor, >> >> I used the solved one as the input model. The space group of the solved >> crystals are: P1 21 1, and P 21. >> >> I will turn the anomalous processing off. >> >> Thanks, >> >> Shen >> >> On Mon, Nov 11, 2019 at 10:40 AM Eleanor Dodson < >> eleanor.dod...@york.ac.uk> wrote: >> >>> Why dont you use one of your solved structures as a model? >>> What space group are the solved ones in? >>> The split spots are not good, but they are well separated and >>> integration programs are not bad at such spacings? And your R merges etc >>> look OK. >>> Just a Q - why turn off the anomalous processing. You dont need to use >>> it, but at some point it may help you find Ss or Ca or whatever.. >>> Eleanor >>> >>> >>> On Mon, 11 Nov 2019 at 15:24, Xu, Shenyuan <x...@miamioh.edu> wrote: >>> >>>> Dear All, >>>> >>>> Thanks for all of your nice suggestions! (Sorry I did not respond to >>>> individual email to say Thanks.) I have used phaser to go through all >>>> possible space groups in the same point group(choose "all possible in same >>>> pointgroup" in the space group menu). I also try P43212 alone. The best >>>> result I get from phaser is (Top LLG: 26.490, Top TFZ: 6.7, Spacegroup: P41 >>>> 2 2), and refinement ends in the R-work: ~0.54, R-free:~0.57. >>>> >>>> I go back to see the diffraction data, and it seems that spots in the >>>> high resolution bin are severely split (pictures are attached). I feel like >>>> the fail of replacement is caused by this. Is this caused by twinning? >>>> >>>> I am looking forward suggestions! >>>> >>>> Thanks, >>>> >>>> Shenyuan Xu >>>> >>>> On Wed, Nov 6, 2019 at 2:58 PM Kay Diederichs < >>>> kay.diederi...@uni-konstanz.de> wrote: >>>> >>>>> Dear Shenyuan, >>>>> >>>>> it seems you assumed P41 21 2 is correct but it isn't - did you try >>>>> P43 21 2 in molecular replacement? >>>>> >>>>> The pointless log file mentions this alternative a few lines above the >>>>> ones you've quoted. >>>>> >>>>> If that does not work, try the other P4x 2y 2 space groups. All of >>>>> this can be done in a single phaser run (choose "all possible in same >>>>> pointgroup" in the space group menu). >>>>> >>>>> Why did you cut the data at 2.29A? They are very strong in the high >>>>> resolution shell! >>>>> >>>>> HTH, >>>>> Kay >>>>> >>>>> On Wed, 6 Nov 2019 14:29:13 -0500, Xu, Shenyuan <x...@miamioh.edu> >>>>> wrote: >>>>> >>>>> >Dear all, >>>>> > >>>>> >I am working on a protein-glycan complex trying to use molecular >>>>> >replacement.This protein is a VP8* domain from rotavirus, adopting a >>>>> >classical galectin-like fold. I already used MR to solve some other >>>>> strains >>>>> >(apo-form and complex form). However, When I want to use the same >>>>> model to >>>>> >solve this particular strain (sequence identity > 95%), MR seems to be >>>>> >failed with R=0.54, Free R = 0.57, and the model does not agree with >>>>> the >>>>> >electron density map once viewed on coot. One difference of this >>>>> >protein-glycan complex between others is that the glycan is longer, >>>>> which >>>>> >has six carbohydrate unit. >>>>> > >>>>> >I used imosflm trying to reindex and use pointless to check the space >>>>> >group, it usually ends up with the current choice: >>>>> >25_pointless.log >>>>> > >>>>> >WARNING! one or more zones have data systematically missing from the >>>>> input >>>>> >file >>>>> >thus we cannot determine if reflections are truly systematically >>>>> absent >>>>> > >>>>> >Best Solution: space group P 41 21 2 >>>>> >Reindex operator: [h,k,l] >>>>> >Laue group probability: 1.000 >>>>> >Systematic absence probability: 0.995 >>>>> >Total probability: 0.995 >>>>> >Space group confidence: 0.993 >>>>> >Laue group confidence 1.000 >>>>> > >>>>> >WARNING: You will have to resolve the enantiomorphic ambiguity later >>>>> > >>>>> >Unit cell: 106.78 106.78 138.59 90.00 90.00 90.00 >>>>> > >>>>> >84.58 to 2.43 - Resolution range used for Laue group search >>>>> > >>>>> >84.58 to 2.29 - Resolution range in file, used for systematic absence >>>>> check >>>>> > >>>>> >Number of batches in file: 1 >>>>> > >>>>> >The data do not appear to be twinned, from the L-test >>>>> >I also use Zanuda to validate the space group, it ends with the same >>>>> choice: >>>>> > >>>>> >Step 3. >>>>> > Refinement of the best model. >>>>> > Candidate symmetry elements are added one by one. >>>>> > >>>>> > current time: Nov 06 16:17 >>>>> GMT >>>>> > expected end of job: Nov 06 17:06 >>>>> GMT >>>>> > >>>>> > >>>>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >>>>> > | >> 3 | C 1 2 1 | 0.3736 | 0.5334 | 0.5044 | >>>>> 0.5586 | >>>>> > >>>>> --------------------------------------------------------------------- >>>>> > | 1 | P 1 | 0.4058 | 0.5318 | 0.5020 | >>>>> 0.5624 | >>>>> > | 5 | P 1 21 1 | 0.4928 | -- | 0.4973 | >>>>> 0.5701 | >>>>> > | 9 | P 21 21 21 | 0.5470 | -- | 0.5011 | >>>>> 0.5736 | >>>>> > | 10 | P 41 21 2 | 0.5749 | -- | 0.5018 | >>>>> 0.5778 | >>>>> > >>>>> --------------------------------------------------------------------- >>>>> > | << 10 | P 41 21 2 | 0.5749 | -- | 0.5018 | >>>>> 0.5778 | >>>>> > >>>>> --------------------------------------------------------------------- >>>>> > >>>>> > R-factor in the original subgroup is (almost) the best. >>>>> > The original spacegroup assignment seems to be correct. >>>>> > >>>>> > The statistics of the dataset seems good: >>>>> >Summary data for Project: Test Crystal: A Dataset: 1 >>>>> > >>>>> > Overall InnerShell >>>>> OuterShell >>>>> >Low resolution limit 84.58 84.58 2.41 >>>>> >High resolution limit 2.29 7.23 2.29 >>>>> > >>>>> >Rmerge (within I+/I-) 0.086 0.036 0.564 >>>>> >Rmerge (all I+ and I-) 0.088 0.036 0.581 >>>>> >Rmeas (within I+/I-) 0.093 0.039 0.610 >>>>> >Rmeas (all I+ & I-) 0.092 0.038 0.604 >>>>> >Rpim (within I+/I-) 0.036 0.015 0.230 >>>>> >Rpim (all I+ & I-) 0.026 0.011 0.165 >>>>> >Rmerge in top intensity bin 0.045 - - >>>>> >Total number of observations 466972 14511 70743 >>>>> >Total number unique 37007 1338 5297 >>>>> >Mean((I)/sd(I)) 20.4 44.5 5.0 >>>>> >Mn(I) half-set correlation CC(1/2) 0.999 0.999 0.947 >>>>> >Completeness 100.0 100.0 100.0 >>>>> >Multiplicity 12.6 10.8 13.4 >>>>> >Mean(Chi^2) 0.97 0.85 0.86 >>>>> > >>>>> >Anomalous completeness 100.0 100.0 100.0 >>>>> >Anomalous multiplicity 6.5 6.6 6.7 >>>>> >DelAnom correlation between half-sets -0.172 -0.180 -0.083 >>>>> >Mid-Slope of Anom Normal Probability 0.857 - - >>>>> > >>>>> >Anomalous flag switched OFF in input, anomalous signal is weak >>>>> > >>>>> >Estimates of resolution limits: overall >>>>> > from half-dataset correlation CC(1/2) > 0.30: limit = 2.29A == >>>>> >maximum resolution >>>>> > from Mn(I/sd) > 2.00: limit = 2.29A == >>>>> >maximum resolution >>>>> > from Mn(I/sd) > 2.00: limit = 2.29A == >>>>> >maximum resolution >>>>> > >>>>> >Estimates of resolution limits in reciprocal lattice directions: >>>>> > Along h k plane >>>>> > from half-dataset correlation CC(1/2) > 0.30: limit = 2.29A == >>>>> >maximum resolution >>>>> > from Mn(I/sd) > 2.00: limit = 2.29A == >>>>> >maximum resolution >>>>> > Along l axis >>>>> > from half-dataset correlation CC(1/2) > 0.30: limit = 2.29A == >>>>> >maximum resolution >>>>> > from Mn(I/sd) > 2.00: limit = 2.29A == >>>>> >maximum resolution >>>>> > >>>>> >Anisotropic deltaB (i.e. range of principal components), A^2: 6.03 >>>>> > >>>>> >Average unit cell: 106.78 106.78 138.59 90.00 90.00 90.00 >>>>> >Space group: P 41 21 2 >>>>> >Average mosaicity: 0.27 >>>>> > >>>>> >Minimum and maximum SD correction factors: Fulls 1.00 1.35 >>>>> Partials >>>>> >0.00 0.00 >>>>> > >>>>> >Any suggestions are welcomed! >>>>> > >>>>> >Thanks, >>>>> > >>>>> >Shenyuan Xu >>>>> > >>>>> >>>>> >######################################################################## >>>>> > >>>>> >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 >>>> >>> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
