|
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
|
| Rmerge
|
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
|
| Rmerge
|
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
|
| Rmerge
|
0.068 (0.22)
|
| Software used
|
DENZO, SCALEPACK (Otwinoski & Minor, 1997)
|
|
|
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