Data quality metrics extracted from 9cqg.cif.gz by aB_cif2table1 from BUSTER (Global Phasing Ltd.). See also the PDBx/mmCIF dictionary and a MXLIMS-compatible JSON representation.


Experimental information for 9CQG 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 17-ID
  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
17-ID
  Synchrotron beamline.
Temperature [K]
_diffrn.ambient_temp
100
  The mean temperature in kelvins at which the intensities were
  measured.
Detector technology
_diffrn_detector.detector
PIXEL
  The general class of the radiation detector.
Collection date
_diffrn_detector.pdbx_collection_date
2021-03-18
  The date of data collection.
Detector
_diffrn_detector.type
DECTRIS EIGER2 X 9M
  The make, model or name of the detector device used.
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
1.0
  Comma separated list of wavelengths or wavelength range.
Software
Data processing
_software.classification
autoPROC
  The classification of the program according to its
  major function.
Data reduction
_software.classification
XDS (Feb 5, 2021)
  The classification of the program according to its
  major function.
Data scaling #1
_software.classification
Aimless (0.7.4)
  The classification of the program according to its
  major function.
Data scaling #2
_software.classification
STARANISO (2.3.63)
  The classification of the program according to its
  major function.
Phasing
_software.classification
PHASER
  The classification of the program according to its
  major function.
Refinement
_software.classification
BUSTER (2.11.8)
  The classification of the program according to its
  major function.
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 1
  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}
87.299
  Unit-cell length a corresponding to the structure reported in
  angstroms.
91.995
  Unit-cell length b corresponding to the structure reported in
  angstroms.
123.580
  Unit-cell length c corresponding to the structure reported in
  angstroms.
85.23
  Unit-cell angle alpha of the reported structure in degrees.
70.69
  Unit-cell angle beta of the reported structure in degrees.
83.23
  Unit-cell angle gamma of the reported structure in degrees.
Wavelength
_diffrn_radiation_wavelength.wavelength
1.00000
  The radiation wavelength in angstroms.
 Å

Diffraction limits
_reflns.pdbx_aniso_diffraction_limit_{1,2,3}
Principal axes of ellipsoid fitted to diffraction cut-off surface
_reflns.pdbx_aniso_diffraction_limit_axis_{1,2,3}_ortho[1..3]
3.041
  Anisotropic diffraction limit along principal axis 1 (of
  ellipsoid fitted to the diffraction cut-off surface).
 Å
0.8277
  Principal axis 1 (X component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
-0.4190
  Principal axis 1 (Y component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
0.3733
  Principal axis 1 (Z component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
2.647
  Anisotropic diffraction limit along principal axis 2 (of
  ellipsoid fitted to the diffraction cut-off surface)
 Å
0.4889
  Principal axis 2 (X component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
0.8650
  Principal axis 2 (Y component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
-0.1131
  Principal axis 2 (Z component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
2.473
  Anisotropic diffraction limit along principal axis 3 (of
  ellipsoid fitted to the diffraction cut-off surface)
 Å
-0.2755
  Principal axis 3 (X component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
0.2761
  Principal axis 3 (Y component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.
0.9208
  Principal axis 3 (Z component) of ellipsoid fitted to the
  diffraction cut-off surface. The applicable orthogonalization
  convention is that specified by
  _reflns.pdbx_orthogonalization_convention.

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å]
_reflns.d_resolution_low _reflns_shell.d_res_low
116.500
  The largest value in angstroms for the interplanar spacings
  for the reflection data. This is called the lowest resolution.
116.500
  The highest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the lowest
  resolution.
2.709
  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
2.474
  The smallest value in angstroms for the interplanar spacings
  for the reflection data. This is called the highest resolution.
6.992
  The smallest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the highest
  resolution.
2.474
  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
0.085
  The R value for merging intensities satisfying the observed
  criteria in this data set.
0.038
  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
0.786
  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
_reflns.pdbx_Rrim_I_all _reflns_shell.pdbx_Rrim_I_all
0.106
  The redundancy-independent merging R factor value Rrim,
  also denoted Rmeas, for merging all intensities in this
  data set.
  
  sum~i~ [N~i~/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
  Rrim = ----------------------------------------------------
  sum~i~ ( sum~j~ I~j~ )
  
  I~j~ = the intensity of the jth observation of reflection i
  <I~i~> = the mean of the intensities of all observations of
  reflection i
   N~i~ = the redundancy (the number of times reflection i
  has been measured).
  
  sum~i~ is taken over all reflections
  sum~j~ is taken over all observations of each reflection.
  
  Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
  Biol. 4, 269-275.
  Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
  30, 203-205.
  Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
0.047
  The redundancy-independent merging R factor value Rrim,
  also denoted Rmeas, for merging all intensities in a
  given shell.
  
  sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
  Rrim = --------------------------------------------------------
  sum~i~ ( sum~j~ I~j~ )
  
  I~j~ = the intensity of the jth observation of reflection i
  <I~i~> = the mean of the intensities of all observations of
  reflection i
   N~i~ = the redundancy (the number of times reflection i
  has been measured).
  
  sum~i~ is taken over all reflections
  sum~j~ is taken over all observations of each reflection.
  
  Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
  Biol. 4, 269-275.
  Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
  30, 203-205.
  Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
0.988
  The redundancy-independent merging R factor value Rrim,
  also denoted Rmeas, for merging all intensities in a
  given shell.
  
  sum~i~ [N~i~ /( N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
  Rrim = --------------------------------------------------------
  sum~i~ ( sum~j~ I~j~ )
  
  I~j~ = the intensity of the jth observation of reflection i
  <I~i~> = the mean of the intensities of all observations of
  reflection i
   N~i~ = the redundancy (the number of times reflection i
  has been measured).
  
  sum~i~ is taken over all reflections
  sum~j~ is taken over all observations of each reflection.
  
  Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
  Biol. 4, 269-275.
  Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
  30, 203-205.
  Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
Rpim
_reflns.pdbx_Rpim_I_all _reflns_shell.pdbx_Rpim_I_all
0.061
  The precision-indicating merging R factor value Rpim,
  for merging all intensities in this data set.
  
  sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
  Rpim = --------------------------------------------------
  sum~i~ ( sum~j~ I~j~ )
  
  I~j~ = the intensity of the jth observation of reflection i
  <I~i~> = the mean of the intensities of all observations
  of reflection i
  N~i~ = the redundancy (the number of times reflection i
  has been measured).
  
  sum~i~ is taken over all reflections
  sum~j~ is taken over all observations of each reflection.
  
  Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
  Biol. 4, 269-275.
  Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
  30, 203-205.
  Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
0.027
  The precision-indicating merging R factor value Rpim,
  for merging all intensities in a given shell.
  
  sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
  Rpim = --------------------------------------------------
  sum~i~ ( sum~j~ I~j~ )
  
  I~j~ = the intensity of the jth observation of reflection i
  <I~i~> = the mean of the intensities of all observations of
  reflection i
  N~i~ = the redundancy (the number of times reflection i
  has been measured).
  
  sum~i~ is taken over all reflections
  sum~j~ is taken over all observations of each reflection.
  
  Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
  Biol. 4, 269-275.
  Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
  30, 203-205.
  Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
0.590
  The precision-indicating merging R factor value Rpim,
  for merging all intensities in a given shell.
  
  sum~i~ [1/(N~i~ - 1)]1/2^ sum~j~ | I~j~ - <I~i~> |
  Rpim = --------------------------------------------------
  sum~i~ ( sum~j~ I~j~ )
  
  I~j~ = the intensity of the jth observation of reflection i
  <I~i~> = the mean of the intensities of all observations of
  reflection i
  N~i~ = the redundancy (the number of times reflection i
  has been measured).
  
  sum~i~ is taken over all reflections
  sum~j~ is taken over all observations of each reflection.
  
  Ref: Diederichs, K. & Karplus, P. A. (1997). Nature Struct.
  Biol. 4, 269-275.
  Weiss, M. S. & Hilgenfeld, R. (1997). J. Appl. Cryst.
  30, 203-205.
  Weiss, M. S. (2001). J. Appl. Cryst. 34, 130-135.
Total number of observations
_reflns.pdbx_number_measured_all
233970
  Total number of measured reflections.
- -
Total number unique
_reflns.number_obs _reflns_shell.number_unique_obs
89165
  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.
5591
  The total number of measured reflections classified as 'observed'
  (see _reflns.observed_criterion) which are symmetry-unique
  after merging for this shell.
4158
  The total number of measured reflections classified as 'observed'
  (see _reflns.observed_criterion) which are symmetry-unique
  after merging for this shell.
<I/σ(I)>
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
7.87
  The mean of the ratio of the intensities to their
  standard uncertainties, <I/sigma(I)>.
18.24
  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.
1.50
  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 (spherical) [%]
_reflns.pdbx_percent_possible_spherical
69.4
  Completeness (as a percentage) of symmetry-unique data
  within the sphere defined by the diffraction limits
  (_reflns.d_resolution_high and
  _reflns.d_resolution_low) relative to all possible
  symmetry-unique reflections within that sphere.
  
  In the absence of an anisotropy description this is
  identical to _reflns.percent_possible_obs.
- -
Completeness (ellipsoidal) [%]
_reflns.pdbx_percent_possible_ellipsoidal
90.9
  Completeness (as a percentage) of symmetry-unique data
  within the intersection of (1) a sphere (defined by the
  diffraction limits, _reflns.d_resolution_high and
  _reflns.d_resolution_low) and (2) the ellipsoid
  (described by __reflns.pdbx_aniso_diffraction_limit_*
  items), relative to all possible symmetry-unique
  reflections within that intersection.
- -
Multiplicity
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
2.6
  Overall redundancy for this data set.
2.8
  Redundancy for the current shell.
2.6
  Redundancy for the current shell.
CC(1/2)
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
0.995
  The Pearson's correlation coefficient expressed as a decimal value
  between the average intensities from randomly selected
  half-datasets.
  
   Ref: Karplus & Diederichs (2012), Science 336, 1030-33
0.996
  The Pearson's correlation coefficient expressed as a decimal value
  between the average intensities from randomly selected
  half-datasets within the resolution shell.
  
   Ref: Karplus & Diederichs (2012), Science 336, 1030-33
0.455
  The Pearson's correlation coefficient expressed as a decimal value
  between the average intensities from randomly selected
  half-datasets within the resolution shell.
  
   Ref: Karplus & Diederichs (2012), Science 336, 1030-33
Anomalous completeness (spherical)
_reflns.pdbx_percent_possible_spherical_anomalous
62.1
  Completeness (as a percentage) of symmetry-unique
  anomalous difference data within the sphere defined by
  the diffraction limits (_reflns.d_resolution_high and
  _reflns.d_resolution_low) relative to all possible
  symmetry-unique anomalous difference data within that
  sphere.
  
  In the absence of an anisotropy description this is
  identical to _reflns.pdbx_percent_possible_anomalous.
- -
Anomalous completeness (ellipsoidal)
_reflns.pdbx_percent_possible_ellipsoidal_anomalous
81.4
  Completeness (as a percentage) of symmetry-unique
  anomalous difference data within the intersection of
  (1) a sphere (defined by the diffraction limits,
  _reflns.d_resolution_high and _reflns.d_resolution_low)
  and (2) the ellipsoid (described by
  __reflns.pdbx_aniso_diffraction_limit_* items),
  relative to all possible symmetry-unique anomalous
  difference data within that intersection.
- -
Anomalous multiplicity
_reflns.pdbx_redundancy_anomalous
1.4
  The overall redundancy of anomalous difference data
  within the sphere defined by the diffraction limits
  (_reflns.d_resolution_high and
  _reflns.d_resolution_low), i.e. data for which
  intensities for both instances of a Friedel pair are
  available for an acentric reflection.
- -
CC(ano)
_reflns.pdbx_CC_half_anomalous
-0.099
  The overall correlation coefficient between two randomly
  chosen half-sets of anomalous intensity differences,
  I(+)-I(-) for anomalous data within the sphere defined
  by the diffraction limits (_reflns.d_resolution_high and
  _reflns.d_resolution_low), i.e. data for which
  intensities for both instances of a Friedel pair are
  available for an acentric reflection.
- -
|DANO|/σ(DANO)
_reflns.pdbx_absDiff_over_sigma_anomalous
0.791
  The overall mean ratio of absolute anomalous intensity
  differences to their standard deviation within the
  sphere defined by the diffraction limits
  (_reflns.d_resolution_high and
  _reflns.d_resolution_low) and using data for which
  intensities for both instances of a Friedel pair are
  available for an acentric reflection.
  
  |Dano|
  -------------
  sigma(Dano)
  
  with
  
  Dano = I(+) - I(-)
  sigma(Dano) = sqrt( sigma(I(+))^2 + sigma(I(-))^2 )
- -

Refinement
PDB entry ID
_entry.id
9CQG
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2024-07-19
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
116.5 - 2.474 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.2435 / 0.2640
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
WARNING: no starting model (for MR) given