The examples here are intended to explain the use of items for describing
phasing data sets in molecule replacement methodologies, using data items
in the PHASING_MR and related categories.
Example 1:
The crystal structure of a double-stranded DNA octamer complexed with
a bacterial antibiotic was solved by molecular replacement based on
the structure of the same duplex octamer with a different antibiotic
and data collected to 3 Å at beamline X13 at EMBL/DESY, Hamburg.
Brief details of the data collection for this phasing set are provided
in the (single) entry in the PHASING_SET category, which is referenced by the
_phasing_set.id item.
The structure was refined based on a data set collected to much higher
resolution at the same beamline at a later date. The search model was
referenced, but the four-letter code identifying the deposition in the
database was not provided.
_phasing.method MR
_refine.pdbx_starting_model 'Wang et al. (1986)'
_pdbx_phasing_MR.model_details 'none, used as is '
_computing.structure_solution 'EPMR (Kissinger et al., 1999)'
loop_
_phasing_set.id
_phasing_set.radiation_source_specific
_phasing_set.radiation_wavelength
_phasing_set.temp
_phasing_set.pdbx_temp_details
_phasing_set.pdbx_d_res_low
_phasing_set.pdbx_d_res_high
1 'beamline X13, EMBL/DESY, Hamburg' 0.8126 100 . 20 3
How this example will appear in the journal
| Data collection |
| Phasing |
| Phasing method
|
Molecular replacement
|
| Starting model data set
|
Wang et al. (1986)
|
| Solution software
|
EPMR (Kissinger et al., 1999)
|
|
|
|
| Phasing set | |
| Radiation source |
Beamline X13, EMBL/DESY, Hamburg |
| Wavelength (Å) (K) |
0.8126 |
| Temperature (K) |
100 |
| Resolution range (Å) |
20-3 |
|
|
|
|
| Alterations to the search model
|
None, used as is
|
|
Example 2:
The crystal structure of a different double-stranded DNA octamer
complexed with the same bacterial antibiotic as Example 1 was also
solved by molecular replacement based on the same structure with a
different antibiotic that was used above. Data collected to
2.1 Å at beamline X13 at EMBL/DESY, Hamburg were used to
solve and refine the structure.
Because the same data set was used for phasing and refinement,
the PHASING_SET category is not used to record brief details of
data collection: full details are available in the DIFFRN group
of categories that characterize the refinement data set. In this
case the value of
_phasing_set.id
is '.' to indicate that no other data set need be considered.
_refine.pdbx_starting_model 'Wang et al. (1986)'
_phasing_set.id .
_pdbx_phasing_MR.model_details 'antibiotic removed from search model'
_computing.structure_solution 'EPMR (Kissinger et al., 1999)'
How this example will appear in the journal
| Data collection |
| Phasing |
| Phasing method
|
Molecular replacement
|
| Starting model data set
|
Wang et al. (1986)
|
| Solution software
|
EPMR (Kissinger et al., 1999)
|
| Alterations to the search model
|
Antibiotic removed from search model
|
|
|
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