data for structural and crystallization communications - example

Example: molecular-replacement phasing

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



Follow Acta Cryst. F
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds