data for structural and crystallization communications - example

Example: MIR phasing

The examples here are intended to explain the use of items for describing phasing data sets in MIR/MIRAS/SIR/SIRAS methodologies, using data items in the PHASING_MIR and related categories.

Example 1: The crystal structure of a human nucleotide kinase was solved by use of a samarium derivative and the SIRAS method. Data were collected in-house for both the native and derivative enzymes on a rotating anode producing Cu Kα radiation (these are the sets labelled 1 and 2 respectively in the _phasing_set.* loop), and the structure was refined against a data set collected at a synchrotron.

In this example, the characteristics of the derivative are shown alongside those of the native data set used for phasing in the loop structure of _phasing_MIR_der.* items. (The internal flags _phasing_MIR_der.native_set_id and _phasing_MIR_der.der_set_id point respectively to the native and derivative data sets summarised in the _phasing_set.* loop.)

In the examples below, the items in gray are identifiers and qualifiers needed to preserve the mmCIF data structure (and auto-generated during the deposition procedure), or other data items stored in the same category in a PDB deposition, but not normally published in the journal.

_phasing.method                         SIRAS
_phasing_MIR.pdbx_number_derivatives    1 
_phasing_MIR.details
;     Native and derivative data sets for phasing were both collected
      in house. A distinct native data set, collected at a synchrotron,
      was used for refinement.
;
_phasing_MIR.d_res_low                  50.0
_phasing_MIR.d_res_high                 2.5
_phasing_MIR.FOM                        0.735
_phasing_MIR.FOM_centric                .
_phasing_MIR.FOM_acentric               .
_computing.structure_solution  
                    'MLPHARE (Otwinowski, 1991), DM (Cowtan & Zhang, 1999)'
_phasing_MIR.method                      'SnB (Weeks et al., 1994)'

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    'RUH3R rot. anode (50 kV, 100 mA)'   1.5418   100   .  100   2.0
        2    'RUH3R rot. anode (50 kV, 100 mA)'   1.5418   100   .   50   2.5

loop_
    _phasing_MIR_der.id
    _phasing_MIR_der.der_set_id
    _phasing_MIR_der.native_set_id
    _phasing_MIR_der.power_acentric
    _phasing_MIR_der.power_centric
    _phasing_MIR_der.details  
       'native for phasing'   .   1   ?   ?   .
       'samarium acetate'     2   .   ?   ?
         '1 h in 20% PEG8000, 0.15M samarium acetate, 100mM Tris-HCl, pH 7.0'

How this example will appear in the journal

Data collection

The refinement data set was also employed in phasing.

Phasing

Phasing method

SIRAS, SnB (Weeks et al., 1990)

No. of derivatives

Phasing strategy

Native and derivative data sets for phasing were both collected in house. A distinct native data set, collected at a synchrotron, was used for refinement.

Resolution range of phasing (Å)

50-2.5

Figure of merit all data

0.735

Solution software

MLPHARE (Otwinowski, 1991), DM (Cowtan & Zhang, 1999)

Phasing set	Native for phasing	Samarium acetate
Radiation source	RUH3R rot. anode (50 kV, 100 mA)	RUH3R rot. anode (50 kV, 100 mA)
Wavelength (Å) (K)	1.5418	1.5418
Temperature (K)	100	100
Resolution range (Å)	100-2.0	50-2.5
Preparation		1 h in 20% PEG8000, 0.15M samarium acetate, 100mM Tris-HCl, pH 7.0

Example 2: As Example 1, but where the native data set is also used for refinement. The data set is more completely characterized in Subsection 2.1 and need not be further treated by items in this Subsection.

In this example the PHASING_SET category therefore contains a brief summary of only the phasing data set collected from the derivative.

In this example, the items in both the PHASING_MIR_DER and PHASING_SET categories appear as single (non-looped) lists. However, they could equally well appear in the mmCIF as looped lists with single rows of entries.

_phasing.method                          SIRAS
_phasing_MIR.pdbx_number_derivatives     1 
_phasing_MIR.details
;     A native data set, collected at a synchrotron, was used both
      for phasing and refinement. Only brief details of data collection
      for the derivative data set are summarized here.
;
_phasing_MIR.FOM                         0.735
_phasing_MIR.FOM_centric                 .
_phasing_MIR.FOM_acentric                .
                    'MLPHARE (Otwinowski, 1991), DM (Cowtan & Zhang, 1999)'
_phasing_MIR.method                      'SnB (Weeks et al., 1994)'

_phasing_MIR_der.id                      'samarium acetate'
_phasing_MIR_der.der_set_id              1
_phasing_MIR_der.native_set_id           .
_phasing_MIR_der.power_acentric          .
_phasing_MIR_der.power_centric           .
_phasing_MIR_der.details
       '1 h in 20% PEG8000, 0.15M samarium acetate, 100mM Tris-HCl, pH 7.0'

_phasing_set.id                          1
_phasing_set.radiation_source_specific   'RUH3R rot. anode (50 kV, 100 mA)' 
_phasing_set.radiation_wavelength        1.5418 
_phasing_set.temp                        100 
_phasing_set.pdbx_temp_details           .
_phasing_set.pdbx_d_res_low              50 
_phasing_set.pdbx_d_res_high             2.5