data for structural and crystallization communications - example

Example: MAD and SAD phasing

The example is intended to explain the use of items providing brief descriptions of the phasing data sets in single- or multiple-wavelength anomalous dispersion methodologies, using data items in the PHASING_MAD and related categories.

Example 1: The crystal structure of a stretch of double-stranded DNA with a drug molecule bound was solved by MAD phasing that took advantage of a single brominated uracil residue in each strand. Four data sets were collected at four wavelengths in the vicinity of the Br K edge at 100K at beamline BW7B at the EMBL outstation at DESY, Hamburg.

One of the data sets, the second, was chosen as the refinement set by virtue of its overall superior quality and is described in detail by use of the items of Subsection 2.1. The insertion for data set 2 is thus partially redundant because that data set is characterized in much more detail by items in the preceding Subsection 2.1 pertaining to the refinement data set. On the other hand, if the refinement set were to be collected at a later date and thus not used for phasing, while the stream of data and contents below would be identically the same, the partial redundancy would be removed because the data set used for phasing would be described nowhere else.

In the example below, the phasing power and FOM items are marked as unknown since they were absent from the report on which the example is based. In practice, recording of these results is highly desirable. The variety of values used here and the variety of data inserted at the temperature-details item further along are intended to illustrate the range of data possible for these items.

_phasing.method                        MAD
_phasing_MAD.method                    standard
_phasing_MAD.details                   'Br-uracil included in the DNA oligomer'
_phasing_MAD.pdbx_anom_scat_method     'SHELXD (Schneider & Sheldrick, 2002)
_phasing_MAD.pdbx_number_sets          4
_phasing_MAD.pdbx_d_res_low            20
_phasing_MAD.pdbx_d_res_high           2.5
_phasing_MAD.pdbx_power_centric        ? 
_phasing_MAD.pdbx_power_acentric       .
_phasing_MAD.pdbx_fom                  ?
_phasing_MAD.pdbx_fom_centric          ?
_phasing_MAD.pdbx_fom_acentric         ?
_computing.structure_solution          'SHELXE (Sheldrick, 2002)'

 1  'BW7B, EMBL c/o DESY, Hamburg'   0.8463   100   .
 2  'BW7B, EMBL c/o DESY, Hamburg'   0.9196   100   'Oxford Cryostream'
 3  'BW7B, EMBL c/o DESY, Hamburg'   0.9204   100   .
 4  'BW7B, EMBL c/o DESY, Hamburg'   0.9050   100   'liquid N2 gas stream'

 1   20        2.5
 2   20        2.4
 3   20        2.4
 4   20        2.5

 1   -1.50     3.20
 2   -6.14     4.34
 3   -8.50     3.80
 4   -3.33     3.70

How this example will appear in the journal

Phasing method MAD, standard
Insertion of scatterers Br-uracil included in the DNA oligomer
Method of locating scatterers SHELXD (Schneider & Sheldrick, 2002)
No. of sets used in phasing 4
Phasing resolution range (Å) 20-2.5
Solution software SHELXE (Sheldrick, 2002)
Phasing set0.8463 Å0.9196 Å0.9204 Å0.9050 Å
Radiation source BW7B, EMBL c/o DESY, Hamburg BW7B, EMBL c/o DESY, Hamburg BW7B, EMBL c/o DESY, Hamburg BW7B, EMBL c/o DESY, Hamburg
Temperature (K) 100 100 (Oxford Cryostream) 100 100 (liquid N2 gas stream)
Resolution range (Å) 20-2.5 20-2.4 20-2.4 20-2.5
f',  f'' -1.50, 3.20 -6.14, 4.34 -8.50, 3.80 -3.33, 3.70

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