data for structural and crystallization communications - example

Example 1: data collection

Based in part on Krätzner, R., Debreczeni, J. I., Pape, T., Schneider, T. R., Wentzel, A., Kolmar, H., Sheldrick, G. M. & Uson, I. (2005). Structure of Ecballium elaterium trypsin inhibitor II (EETI-II): a rigid molecular scaffold. Acta Cryst. D61, 1255-1262. [1W7Z, 1H9H, 1H91 ].

The examples are based on the determination of structures of trypsin inhibitor EETI-II (1W7Z) and complexes of trypsin with wild-type EETI-II (1H9H) and mutant (1H9I). Data for the inhibitor were collected at BESSY (Berlin), for the trypsin complex with wild-type inhibitor at ESRF (Grenoble), and for the complex with mutant inhibitor on a rotating anode.

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.

Example 1: trypsin inhibitor

# ============================ EETI-II ===================================
_database_2.database_id                       PDB
_database_2.database_code                     1W7Z

_diffrn_radiation.pdbx_diffrn_protocol        'single wavelength'
_diffrn_measurement.device                    'oscillation camera'
_diffrn_measurement.device_details            .
_diffrn_measurement.method                    .
_diffrn_source.source                         'synchrotron'
_diffrn_source.type                           'BESSY (Berlin) BL2'
_diffrn_radiation.monochromator           'Si(111) double-crystal monochromator'
_diffrn_source.size       'focus at crystal; 0.132mm (horiz.) x 0.092mm (vert.)'
_diffrn_radiation.pdbx_wavelength             1.000
_diffrn_radiation.pdbx_wavelength_list        .
_diffrn_detector.detector                     'image plate'
_diffrn_detector.type                         'MAR 345'
_diffrn.ambient_temp                          100.
_diffrn.ambient_temp_esd                      1.5
_diffrn.ambient_temp_details                  .
_diffrn_detector.pdbx_collection_time_total   3960
_diffrn_detector.pdbx_frames_total            270
_computing.data_reduction           'DENZO, SCALEPACK (Otwinoski & Minor, 1997)'
_reflns.d_resolution_low                      30.0
_reflns.d_resolution_high                     1.68
_reflns_shell.d_res_low                       1.80
_reflns_shell.d_res_high                      1.68
_reflns.number_all                            35516
_reflns.details                              'symmetry and Friedel mates merged'
_reflns_shell.number_unique_all               3444
_reflns.percent_possible_obs                  96.8
_reflns_shell.percent_possible_obs            99.0
_reflns.pdbx_redundancy                       4.42
_reflns_shell.pdbx_redundancy                 3.33
_reflns.pdbx_netI_over_sigmaI                 13.7
_reflns_shell.pdbx_netI_over_sigmaI_all       3.1
_reflns_shell.pdbx_netI_over_sigmaI_obs       ?
_reflns.pdbx_res_netI_over_sigmaI_2           1.80
_reflns.Rmerge_F_all                          .
_reflns.Rmerge_F_obs                          .
_reflns_shell.Rmerge_F_all                    .
_reflns_shell.Rmerge_F_obs                    .
_reflns.pdbx_Rmerge_I_all                     0.069
_reflns.pdbx_Rmerge_I_obs                     ?
_reflns_shell.Rmerge_I_all                    0.44
_reflns_shell.Rmerge_I_obs                    ?

How this example will appear in the journal


Table 2. Data collection
Values for the outer shell are given in parentheses.

Diffraction protocol	Single wavelength
Sampling protocol	Oscillation camera
Diffraction source	Synchrotron; BESSY (Berlin) BL2
Monochromator	Si(111) double-crystal monochromator
Wavelength (Å)	1.000
Detector type	Image plate (MAR 345)
Temperature (K)	100.0 (15)
Total measuring time (s)	3960
No. of images	270
Resolution range (Å)	30.0-1.68 (1.80-1.68)
No. of unique reflections	35516 (3444)
Completeness (%)	96.8 (99.0)
Redundancy	4.42 (3.33)
< I/σ(I) >	13.7 (3.1)
d spacing at < I/σ(I) > = 2 (Å)	1.80
R_merge	0.069 (0.44)
Software used	DENZO, SCALEPACK (Otwinoski & Minor, 1997)

Example 2: trypsin + wild-type inhibitor

# ========================== Trypsin + wildtype I =============================
_database_2.database_id                       PDB
_database_2.database_code                     1H9H

_diffrn_radiation.pdbx_diffrn_protocol        'single wavelength'
_diffrn_source.source                         'synchrotron'
_diffrn_measurement.device                    'oscillation camera'
_diffrn_measurement.device_details            .
_diffrn_measurement.method                    .
_diffrn_source.type                           'ESRF (Grenoble) ID14-EH2'
_diffrn_radiation.collimation                 'toroidal focusing mirror'
_diffrn_radiation.monochromator               'diamond(111), Ge(220)'
_diffrn_source.size                           ?
_diffrn_radiation.pdbx_wavelength             0.9326
_diffrn_radiation.pdbx_wavelength_list        .
_diffrn_detector.detector                     'CCD'
_diffrn_detector.type                         'MAR Research'
_diffrn.ambient_temp                          100.
_diffrn.ambient_temp_esd                      ?
_diffrn.ambient_temp_details                  .
_diffrn_detector.pdbx_collection_time_total   ?
_diffrn_detector.pdbx_frames_total            ?
_computing.data_reduction           'DENZO, SCALEPACK (Otwinoski & Minor, 1997)'
_reflns.d_resolution_low                      20.0
_reflns.d_resolution_high                     1.50
_reflns_shell.d_res_low                       1.6
_reflns_shell.d_res_high                      1.5
_reflns.number_all                            49533
_reflns.details                              'symmetry and Friedel mates merged'
_reflns_shell.number_unique_all               3004
_reflns.percent_possible_obs                  99.7
_reflns_shell.percent_possible_obs            99.6
_reflns.pdbx_redundancy                       8.05
_reflns_shell.pdbx_redundancy                 4.48
_reflns.pdbx_netI_over_sigmaI                 19.24
_reflns_shell.pdbx_netI_over_sigmaI_all       3.39
_reflns_shell.pdbx_netI_over_sigmaI_obs       ?
_reflns.pdbx_res_netI_over_sigmaI_2           1.52
_reflns.Rmerge_F_all                          .
_reflns.Rmerge_F_obs                          .
_reflns_shell.Rmerge_F_all                    .
_reflns_shell.Rmerge_F_obs                    .
_reflns.pdbx_Rmerge_I_all                     0.53
_reflns.pdbx_Rmerge_I_obs                     ?
_reflns_shell.Rmerge_I_all                    0.396
_reflns_shell.Rmerge_I_obs                    ?

How this example will appear in the journal


Table 2. Data collection
Values for the outer shell are given in parentheses.

Diffraction protocol	Single wavelength
Sampling protocol	Oscillation camera
Diffraction source	Synchrotron; ESRF (Grenoble) ID14-EH2
Focusing and collimation	Toroidal focusing mirror
Monochromator	Diamond(111), Ge(220)
Wavelength (Å)	0.9326
Detector type	CCD (MAR Research)
Temperature (K)	100
Resolution range (Å)	20.0-1.50 (1.6-1.5)
No. of unique reflections	49533 (3004)
Completeness (%)	99.7 (99.6)
Redundancy	8.05 (4.48)
< I/σ(I) >	19.24 (3.39)
d spacing at < I/σ(I) > = 2 (Å)	1.52
R_merge	0.053 (0.40)
Software used	DENZO, SCALEPACK (Otwinoski & Minor, 1997)

Example 3: trypsin + mutant

#============================= Trypsin + mutant ===============================
_database_2.database_id                       PDB
_database_2.database_code                     1H9I

_diffrn_radiation.pdbx_diffrn_protocol        'single wavelength'
_diffrn_measurement.device                    'oscillation camera'
_diffrn_measurement.device_details            .
_diffrn_measurement.method                    .
_diffrn_source.source                         'rotating anode'
_diffrn_source.type                           'MAC M18XHF'
_diffrn_radiation.collimation                 'Osmic mirror system'
_diffrn_source.size                           ?
_diffrn_radiation.pdbx_wavelength             1.5418
_diffrn_radiation.pdbx_wavelength_list        .
_diffrn_detector.detector                     'CCD'
_diffrn_detector.type                         'MAR Research'
_diffrn.ambient_temp                          100.
_diffrn.ambient_temp_esd                      2
_diffrn.ambient_temp_details                  .
_diffrn_detector.pdbx_collection_time_total   21750
_diffrn_detector.pdbx_frames_total            180
_computing.data_reduction           'DENZO, SCALEPACK (Otwinoski & Minor, 1997)'
_reflns.d_resolution_low                      15.0
_reflns.d_resolution_high                     1.90
_reflns_shell.d_res_low                       2.0
_reflns_shell.d_res_high                      1.9
_reflns.number_all                            26024
_reflns.details                              'symmetry and Friedel mates merged'
_reflns_shell.number_unique_all               1798
_reflns.percent_possible_obs                  99.1
_reflns_shell.percent_possible_obs            97.9
_reflns.pdbx_redundancy                       6.6
_reflns_shell.pdbx_redundancy                 6.31
_reflns.pdbx_netI_over_sigmaI                 17.84
_reflns_shell.pdbx_netI_over_sigmaI_all       8.89
_reflns_shell.pdbx_netI_over_sigmaI_obs       ?
_reflns.pdbx_res_netI_over_sigmaI_2           2.1
_reflns.Rmerge_F_all                          .
_reflns.Rmerge_F_obs                          .
_reflns_shell.Rmerge_F_all                    .
_reflns_shell.Rmerge_F_obs                    .
_reflns.pdbx_Rmerge_I_all                     ?
_reflns.pdbx_Rmerge_I_obs                     0.683
_reflns_shell.Rmerge_I_all                    ?
_reflns_shell.Rmerge_I_obs                    0.22

How this example will appear in the journal


Table 2. Data collection
Values for the outer shell are given in parentheses.

Diffraction protocol	Single wavelength
Sampling protocol	Oscillation camera
Diffraction source	Rotating anode; MAC M18XHF
Collimation	Osmic mirror system
Wavelength (Å)	1.5418
Detector type	CCD (MAR Research)
Temperature (K)	100 (2)
Total measuring time (s)	21750
No. of images	180
Resolution range (Å)	15.0-1.90 (2.0-1.9)
No. of unique reflections	26024 (1798)
Completeness (%)	99.1 (97.9)
Redundancy	6.6 (6.31)
< I/σ(I) >	17.84 (8.89)
d spacing at < I/σ(I) > = 2 (Å)	2.1
R_merge	0.068 (0.22)
Software used	DENZO, SCALEPACK (Otwinoski & Minor, 1997)

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data for structural and crystallization communications - example

Example 1: data collection

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