Data quality metrics extracted from 3cdh.cif.gz by aB_cif2table1 from BUSTER (Global Phasing Ltd.). See also the PDBx/mmCIF dictionary.


Experimental information for 3CDH at RCSB, PDBe, PDBj

Experiment
Method
_exptl.method
X-RAY DIFFRACTION
  The method used in the experiment.
Experimental protocol
_diffrn_radiation.pdbx_diffrn_protocol
SINGLE WAVELENGTH
  SINGLE WAVELENGTH, LAUE, or MAD.
Source type
_diffrn_source.source
SYNCHROTRON
  The general class of the radiation source.
Source details
_diffrn_source.type
APS BEAMLINE 19-BM
  The make, model or name of the source of radiation.
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
APS
  Synchrotron site.
Beamline
_diffrn_source.pdbx_synchrotron_beamline
19-BM
  Synchrotron beamline.
Temperature [K]
_diffrn.ambient_temp
100.0
  The mean temperature in kelvins at which the intensities were
  measured.
Detector technology
_diffrn_detector.detector
CCD
  The general class of the radiation detector.
Collection date
_diffrn_detector.pdbx_collection_date
2007-11-21
  The date of data collection.
Detector
_diffrn_detector.type
APS-1
  The make, model or name of the detector device used.
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
0.9793
  Comma separated list of wavelengths or wavelength range.
Software
Data collection #1
_software.classification
SBC-Collect
  The classification of the program according to its
  major function.
Data collection #2
_software.classification
HKL-2000
  The classification of the program according to its
  major function.
Data reduction
_software.classification
HKL-2000
  The classification of the program according to its
  major function.
Data scaling
_software.classification
HKL-2000
  The classification of the program according to its
  major function.
Phasing #1
_software.classification
HKL-3000
  The classification of the program according to its
  major function.
Phasing #2
_software.classification
MLPHARE
  The classification of the program according to its
  major function.
Phasing #3
_software.classification
SHELXD
  The classification of the program according to its
  major function.
Phasing #4
_software.classification
DM
  The classification of the program according to its
  major function.
Phasing #5
_software.classification
RESOLVE
  The classification of the program according to its
  major function.
Model building #1
_software.classification
DM
  The classification of the program according to its
  major function.
Model building #2
_software.classification
RESOLVE
  The classification of the program according to its
  major function.
Model building #3
_software.classification
Coot
  The classification of the program according to its
  major function.
Refinement
_software.classification
REFMAC (5.2.0019)
  The classification of the program according to its
  major function.
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 62 2 2
  Hermann-Mauguin space-group symbol. Note that the
  Hermann-Mauguin symbol does not necessarily contain complete
  information about the symmetry and the space-group origin. If
  used, always supply the FULL symbol from International Tables
  for Crystallography Vol. A (2002) and indicate the origin and
  the setting if it is not implicit. If there is any doubt that
  the equivalent positions can be uniquely deduced from this
  symbol, specify the _symmetry_equiv.pos_as_xyz or
  _symmetry.space_group_name_Hall data items as well. Leave
  spaces between symbols referring to
  different axes.
Unit cell parameters
_cell.length_{a,b,c} _cell.angle_{alpha,beta,gamma}
124.140
  Unit-cell length a corresponding to the structure reported in
  angstroms.
124.140
  Unit-cell length b corresponding to the structure reported in
  angstroms.
140.186
  Unit-cell length c corresponding to the structure reported in
  angstroms.
90.0
  Unit-cell angle alpha of the reported structure in degrees.
90.0
  Unit-cell angle beta of the reported structure in degrees.
120.0
  Unit-cell angle gamma of the reported structure in degrees.
Wavelength
_diffrn_radiation_wavelength.wavelength
0.97930
  The radiation wavelength in angstroms.
 Å

Data quality metricsOverallOuterShell
Low resolution limit [Å]
_reflns.d_resolution_low _reflns_shell.d_res_low
35.370
  The largest value in angstroms for the interplanar spacings
  for the reflection data. This is called the lowest resolution.
2.800
  The highest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the lowest
  resolution.
High resolution limit [Å]
_reflns.d_resolution_high _reflns_shell.d_res_high
2.690
  The smallest value in angstroms for the interplanar spacings
  for the reflection data. This is called the highest resolution.
2.690
  The smallest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the highest
  resolution.
Rmerge
_reflns.pdbx_Rmerge_I_obs _reflns_shell.Rmerge_I_obs
0.115
  The R value for merging intensities satisfying the observed
  criteria in this data set.
0.835
  The value of Rmerge(I) for reflections classified as 'observed'
  (see _reflns.observed_criterion) in a given shell.
  
  sum~i~(sum~j~|I~j~ - <I>|)
  Rmerge(I) = --------------------------
  sum~i~(sum~j~<I>)
  
  I~j~ = the intensity of the jth observation of reflection i
  <I> = the mean of the intensities of all observations of
  reflection i
  
  sum~i~ is taken over all reflections
  sum~j~ is taken over all observations of each reflection
  Rmeas - -
  Rpim - -
  Total number of observations - -
Total number unique
_reflns.number_obs
18036
  The number of reflections in the REFLN list (not the DIFFRN_REFLN
  list) classified as observed (see _reflns.observed_criterion).
  This number may contain Friedel-equivalent reflections according
  to the nature of the structure and the procedures used.
-
<I/σ(I)>
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
7.20
  The mean of the ratio of the intensities to their
  standard uncertainties, <I/sigma(I)>.
2.60
  The ratio of the mean of the intensities of the reflections
  classified as 'observed' (see _reflns.observed_criterion) in
  this shell to the mean of the standard uncertainties of the
  intensities of the 'observed' reflections in this
  shell.
Completeness [%]
_reflns.percent_possible_obs _reflns_shell.percent_possible_all
99.5
  The percentage of geometrically possible reflections represented
  by reflections that satisfy the resolution limits established
  by _reflns.d_resolution_high and _reflns.d_resolution_low and
  the observation limit established by
  _reflns.observed_criterion.
94.2
  The percentage of geometrically possible reflections represented
  by all reflections measured for this shell.
Multiplicity
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
11.9
  Overall redundancy for this data set.
12.6
  Redundancy for the current shell.
  CC(1/2) - -

Refinement
PDB entry ID
_entry.id
3CDH
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2008-02-26
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
35.4 - 2.690 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.2002 / 0.2275
Structure solution method
_refine.pdbx_method_to_determine_struct
SAD