[phenixbb] help on MIR dataset

[Ni, Fengyun]

Hi everyone,

I am working on a MIR dataset: one native data, three EMTS soaked data at different concentration, one PbAc2 data. My initial trial with phenix autosol did not give positive solutions. I hope I could get some information from all of you.

I index and integrate the data in Mosflm and possible group is P3, though the Pointless said the most possible is P3121. But for now, I only tried P3 at different resolutions for the reason that a potential MR solution (below 20% identities, TFZ=7.1) was found in P31 space group. If P3121 is the real space group, the space is too crowed to fit my molecules unless they have some unexpected symmetry.

For the difference among dataset in P3 space group, the output from SCALEIT of CCP4 gives as follows,

 RMS differences|RMSiso      RMSano      
 ----------------------------------------
 FP-hg          |172.30      22.50      
 FP-hg2         |159.20      24.07       
 FP-hg3         |85.08       27.92 
 FP-pb          |31.15       24.55 

The native data's resolution cutoff is 3.2 A, and 3.2/3.8/3.5 for different EMTS data, 3.5 for Pb data.I did notice some radiation damage for EMTS (Hg) data (large negative B-factors in SCALA), but not for Pb data. And the anomalous signal only extend to 5.6 and 4.5 A for EMTS and Pb data, respectively, as indicated by phenix.xtriage. These are all the possible heavy atom data we could obtain. So i tried all of them in phenix.autosol. The input is like follows,

 autosol {
  seq_file = ../seq.dat
  crystal_info {
  solvent_fraction = 0.62  #determined from matthews coefficient to assure "reasonable" content in asymmetric unit. 
  }
  native {
    data = nat.mtz
  }
  deriv {
    data = hg1.mtz
    atom_type = Hg
    inano = noinano *inano anoonly
    lambda = 1.00394
  }
  deriv {
    data = hg2.mtz
    atom_type = Hg
    inano = noinano *inano anoonly
    lambda = 1.00394
  }
  deriv {
    data = hg3.mtz
    atom_type = Hg
    inano = noinano *inano anoonly
    lambda = 1.00394
  }
  deriv {
    data = pb.mtz
    atom_type = Pb
    inano = noinano *inano anoonly
    lambda = 0.94640
  }
  model_building {
    build = False   #my structure is DNA/protein complex, so i choose to stop the building process.
 }
}

I tried at different resolutions, 3.6/4.0/4.4/4.8/5.2/5.6/6.0 A. One solution was given based on Pb data at 4.8 A with following statistics,

Solution # 6  BAYES-CC: 59.7 +/- 17.2 (2SD) Dataset #4   FOM: 0.24
 Score type:       SKEW    CORR_RMS    NCS_OVERLAP
Raw scores:        0.31      0.69      0.00
100x EST OF CC:   59.74     17.55     31.25

Refined heavy atom sites (fractional):
           X         Y          Z
xyz       0.033      0.020      0.538
xyz       0.417      0.217      0.113
xyz       0.041      0.010      0.721


The statistics is almost the same for its inverse, and i read from the output that the statistics for phasing other Hg datasets are very low (BAYES-CC is lower than 20) based on the above solution. The resulting map does not make much sense yet.

Sorry for the long post. Any suggestion is welcome.
Thank you very much!
Fengyun