Data quality metrics extracted from 8ab3.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 8AB3 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
ESRF BEAMLINE ID23-2
  The make, model or name of the source of radiation.
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
ESRF
  Synchrotron site.
Beamline
_diffrn_source.pdbx_synchrotron_beamline
ID23-2
  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
2022-01-28
  The date of data collection.
Detector
_diffrn_detector.type
DECTRIS PILATUS 2M
  The make, model or name of the detector device used.
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
0.87313
  Comma separated list of wavelengths or wavelength range.
Software
Data processing #1
_software.classification
autoPROC (1.0.5 20220608)
  The classification of the program according to its
  major function.
Data processing #2
_software.classification
TRUNCATE (7.1.011)
  The classification of the program according to its
  major function.
Data reduction
_software.classification
XDS (Jan 10, 2022)
  The classification of the program according to its
  major function.
Data scaling
_software.classification
Aimless (0.7.4)
  The classification of the program according to its
  major function.
Phasing
_software.classification
PHENIX (1.19.2-4158)
  The classification of the program according to its
  major function.
Refinement #1
_software.classification
BUSTER (2.10.4 (8-JUN-2022))
  The classification of the program according to its
  major function.
Refinement #2
_software.classification
BUSTER (2.10.4 (8-JUN-2022))
  The classification of the program according to its
  major function.
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 1 21 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}
70.369
  Unit-cell length a corresponding to the structure reported in
  angstroms.
111.504
  Unit-cell length b corresponding to the structure reported in
  angstroms.
101.793
  Unit-cell length c corresponding to the structure reported in
  angstroms.
90.00
  Unit-cell angle alpha of the reported structure in degrees.
99.78
  Unit-cell angle beta of the reported structure in degrees.
90.00
  Unit-cell angle gamma of the reported structure in degrees.
Wavelength
_diffrn_radiation_wavelength.wavelength
0.87313
  The radiation wavelength in angstroms.
 Å

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å]
_reflns.d_resolution_low _reflns_shell.d_res_low
100.314
  The largest value in angstroms for the interplanar spacings
  for the reflection data. This is called the lowest resolution.
100.314
  The highest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the lowest
  resolution.
2.661
  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
2.616
  The smallest value in angstroms for the interplanar spacings
  for the reflection data. This is called the highest resolution.
7.100
  The smallest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the highest
  resolution.
2.616
  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
0.195
  The R value for merging intensities satisfying the observed
  criteria in this data set.
0.081
  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
0.754
  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
0.222
  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.
0.093
  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.
0.853
  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
0.105
  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.
0.045
  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.
0.391
  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 _reflns_shell.number_measured_all
200506
  Total number of measured reflections.
9368
  The total number of reflections measured for this
  shell.
10675
  The total number of reflections measured for this
  shell.
Total number unique
_reflns.number_obs _reflns_shell.number_unique_all
46537
  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.
2324
  The total number of measured reflections which are symmetry-
  unique after merging for this shell.
2342
  The total number of measured reflections which are symmetry-
  unique after merging for this shell.
<I/σ(I)>
_reflns.pdbx_netI_over_sigmaI _reflns_shell.meanI_over_sigI_obs
5.62
  The mean of the ratio of the intensities to their
  standard uncertainties, <I/sigma(I)>.
11.29
  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.
1.99
  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
99.3
  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.
96.1
  The percentage of geometrically possible reflections represented
  by all reflections measured for this shell.
100.0
  The percentage of geometrically possible reflections represented
  by all reflections measured for this shell.
Multiplicity
_reflns.pdbx_redundancy _reflns_shell.pdbx_redundancy
4.3
  Overall redundancy for this data set.
4.0
  Redundancy for the current shell.
4.6
  Redundancy for the current shell.
CC(1/2)
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
0.983
  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
0.991
  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
0.726
  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
_reflns.pdbx_percent_possible_anomalous _reflns_shell.pdbx_percent_possible_anomalous
95.8
  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.
94.0
  Completeness (as a percentage) of symmetry-unique
  anomalous difference data within the spherical shell
  defined by its diffraction limits
  (_reflns_shell.d_resolution_high and
  _reflns_shell.d_resolution_low) relative to all
  possible symmetry-unique anomalous difference data
  within that shell.
98.0
  Completeness (as a percentage) of symmetry-unique
  anomalous difference data within the spherical shell
  defined by its diffraction limits
  (_reflns_shell.d_resolution_high and
  _reflns_shell.d_resolution_low) relative to all
  possible symmetry-unique anomalous difference data
  within that shell.
Anomalous multiplicity
_reflns.pdbx_redundancy_anomalous _reflns_shell.pdbx_redundancy_anomalous
2.2
  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.
2.1
  The redundancy of anomalous difference data within the
  spherical shell (defined by its diffraction limits
  _reflns_shell.d_resolution_high and
  _reflns_shell.d_resolution_low), i.e. data for which
  intensities for both instances of a Friedel pair are
  available for an acentric reflection.
2.3
  The redundancy of anomalous difference data within the
  spherical shell (defined by its diffraction limits
  _reflns_shell.d_resolution_high and
  _reflns_shell.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 _reflns_shell.pdbx_CC_half_anomalous
-0.127
  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.
-0.371
  The correlation coefficient within the spherical shell
  (defined by its diffraction limits
  _reflns_shell.d_resolution_high and
  _reflns_shell.d_resolution_low) between two randomly
  chosen half-sets of anomalous intensity differences,
  I(+)-I(-) for anomalous data, i.e. data for which
  intensities for both instances of a Friedel pair are
  available for an acentric reflection.
-0.030
  The correlation coefficient within the spherical shell
  (defined by its diffraction limits
  _reflns_shell.d_resolution_high and
  _reflns_shell.d_resolution_low) between two randomly
  chosen half-sets of anomalous intensity differences,
  I(+)-I(-) for anomalous data, 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 _reflns_shell.pdbx_absDiff_over_sigma_anomalous
0.745
  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 )
0.584
  The mean ratio of absolute anomalous intensity
  differences to their standard deviation within the
  spherical shell (defined by its diffraction limits
  _reflns_shell.d_resolution_high and
  _reflns_shell.d_resolution_low).
  
  |Dano|
  -------------
  sigma(Dano)
  
  with
  
  Dano = I(+) - I(-)
  sigma(Dano) = sqrt( sigma(I(+))^2 + sigma(I(-))^2 )
0.731
  The mean ratio of absolute anomalous intensity
  differences to their standard deviation within the
  spherical shell (defined by its diffraction limits
  _reflns_shell.d_resolution_high and
  _reflns_shell.d_resolution_low).
  
  |Dano|
  -------------
  sigma(Dano)
  
  with
  
  Dano = I(+) - I(-)
  sigma(Dano) = sqrt( sigma(I(+))^2 + sigma(I(-))^2 )

Refinement
PDB entry ID
_entry.id
8AB3
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2022-07-04
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
100.3 - 2.616 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.1862 / 0.2318
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
4ojn