Re: [ccp4bb] tricky molecular replacement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: tricky molecular replacement
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2007-11-02

Next message:
Subject: Re: Fwd: CCP4i and modeller integration
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-03

Subject: Re: tricky molecular replacement
From: "Edward A {- dot -} Berry" EABerry {- at -} LBL {- dot -} GOV
Date: 2007-11-03

One other idea idea:
1. Solvent flattening on the hexagonal crystal
2. use the flattening mask to cut out the density of one molecule,
put in a large P1 cell for calculating structure factors
3. Use the structure factors from the density of the hexagonal crystal
to solve the triclinic crystal by molecular replacement.
4. If 3 works, multicrystal averaging to improve both crystals
til the map is traceable.

Jan Abendroth wrote:
> Hi all,
> I have a tricky molecular replacement case. One protein in two different
> crystal forms: hexagonal with 1 mol/asu, triclinic with 2 mol/asu (based
> on packing and self rotation).
>
> No experimental phases are available this far, however, there is a
> distant homology model. For the hexagonal crystals, phaser gives a
> solution with really good scores (Z > 9, -LLG > 50) and a good packing.
> While the correct solution is way down the list in the RF, the TF can
> separate it from the bulk of bad solutions. Slight changes in the model
> give the same solution. Maps are somehow ok, however, not good enough to
> enable arpwarp to build the model. It does not totally blow up either.
>
> For the triclinic crystal form with 2 molecules related by a two-fold
> which is not parallel to a crystal axis, phaser does not find a
> solution. Neither does molrep using the locked rotation function with
> the two-fold extracted by the SRF.
>
> As the homology between the data set should be higher than between the
> model in the data sets and the search model, I tried a cross rotation
> function between the two data sets. Strong peaks there should give the
> relation between the orientation of the molecule in the hexagonal
> crystal (that I believe I can find). With two rotations known and one
> translation undefined, I'd be left with only one translation that needs
> to be found. Then averaging within P1 or cross crystal might improve the
> density...
>
> Almn appears to be the only program in ccp4 that can do a cross rotation
> using Fs only, right?? I used the P1 data as hklin, the hexagonal data
> as hklin2. Almn comes back with two strong peaks (see below), however,
> now I am lost:
> - the first two peaks appear to be the same
> - are the Euler angles the ones I could use in a peak list for eg. Phaser?
> - does this procedure make sense at all?
> - any other ideas?
>
> Thanks a lot
> Jan
>
> almn.log:
> ##########
> Peaks must be greater than 2.00 times RMS density 52.2161
>
>
>
> Eulerian angles Polar angles
>
> Alpha Beta Gamma Peak Omega Phi
> Kappa Direction cosines
> PkNo Symm: 1 2
>
> Peak 1
> 1 1 1 323.7 143.4 18.5 540.8 92.9 62.6
> 143.8 0.4594 0.8867 -0.0511
> 1 1 2 323.7 143.4 78.5 540.8 83.2 32.6
> 145.9 0.8364 0.5351 0.1184
> 1 1 3 323.7 143.4 138.5 540.8 75.6 2.6
> 157.2 0.9674 0.0441 0.2495
> 1 1 4 323.7 143.4 198.5 540.8 71.9 332.6
> 174.4 0.8439 -0.4373 0.3108
> 1 1 5 323.7 143.4 258.5 540.8 107.2 122.6
> 167.0 -0.5149 0.8049 -0.2950
> 1 1 6 323.7 143.4 318.5 540.8 101.7 92.6
> 151.7 -0.0446 0.9781 -0.2034
> 1 1 7 143.7 36.6 41.5 540.8 161.7 321.1
> 175.0 0.2448 -0.1974 -0.9493
> 1 1 8 143.7 36.6 341.5 540.8 20.4 171.1
> 128.2 -0.3451 0.0540 0.9370
> 1 1 9 143.7 36.6 281.5 540.8 31.6 201.1
> 73.8 -0.4882 -0.1885 0.8521
> 1 1 10 143.7 36.6 221.5 540.8 82.2 231.1
> 37.0 -0.6220 -0.7711 0.1363
> 1 1 11 143.7 36.6 161.5 540.8 144.3 261.1
> 65.1 -0.0902 -0.5770 -0.8118
> 1 1 12 143.7 36.6 101.5 540.8 158.6 291.1
> 118.5 0.1317 -0.3411 -0.9307
>
> Peak 2
> 2 1 1 143.7 36.6 41.5 540.8 161.7 321.1
> 175.0 0.2448 -0.1974 -0.9493
> 2 1 2 143.7 36.6 101.5 540.8 158.6 291.1
> 118.5 0.1317 -0.3411 -0.9307
> 2 1 3 143.7 36.6 161.5 540.8 144.3 261.1
> 65.1 -0.0902 -0.5770 -0.8118
> 2 1 4 143.7 36.6 221.5 540.8 82.2 231.1
> 37.0 -0.6220 -0.7711 0.1363
> 2 1 5 143.7 36.6 281.5 540.8 31.6 201.1
> 73.8 -0.4882 -0.1885 0.8521
> 2 1 6 143.7 36.6 341.5 540.8 20.4 171.1
> 128.2 -0.3451 0.0540 0.9370
> 2 1 7 323.7 143.4 18.5 540.8 92.9 62.6
> 143.8 0.4594 0.8867 -0.0511
> 2 1 8 323.7 143.4 318.5 540.8 101.7 92.6
> 151.7 -0.0446 0.9781 -0.2034
> 2 1 9 323.7 143.4 258.5 540.8 107.2 122.6
> 167.0 -0.5149 0.8049 -0.2950
> 2 1 10 323.7 143.4 198.5 540.8 71.9 332.6
> 174.4 0.8439 -0.4373 0.3108
> 2 1 11 323.7 143.4 138.5 540.8 75.6 2.6
> 157.2 0.9674 0.0441 0.2495
> 2 1 12 323.7 143.4 78.5 540.8 83.2 32.6
> 145.9 0.8364 0.5351 0.1184
>
> Peak 3
> 3 1 1 335.2 54.5 36.5 209.2 78.8 59.3
> 55.6 0.5006 0.8437 0.1940 ...
> Peak 4
> 4 1 1 155.2 125.5 23.5 209.2 62.8 155.8
> 179.4 -0.8112 0.3638 0.4579 ...
> Peak 5
> 5 1 1 349.3 53.8 13.0 176.4 87.7 78.2
> 53.9 0.2051 0.9779 0.0406 ...

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: tricky molecular replacement
From: Jan Abendroth jan {- dot -} abendroth {- at -} GMAIL {- dot -} COM
Date: 2007-11-02

Next message:
Subject: Re: Fwd: CCP4i and modeller integration
From: "Winn, MD (Martyn)" m {- dot -} d {- dot -} winn {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-11-03