Data quality metrics extracted from 7nnb.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 7NNB 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
DIAMOND BEAMLINE I04
  The make, model or name of the source of radiation.
Synchrotron site
_diffrn_source.pdbx_synchrotron_site
Diamond
  Synchrotron site.
Beamline
_diffrn_source.pdbx_synchrotron_beamline
I04
  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
2017-03-04
  The date of data collection.
Detector
_diffrn_detector.type
DECTRIS PILATUS 6M-F
  The make, model or name of the detector device used.
Wavelength(s) [Å]
_diffrn_source.pdbx_wavelength_list
0.9795
  Comma separated list of wavelengths or wavelength range.
Software
Data reduction
_software.classification
XDS
  The classification of the program according to its
  major function.
Data scaling
_software.classification
Aimless (0.5.31)
  The classification of the program according to its
  major function.
Phasing
_software.classification
PHASER (2.6.0)
  The classification of the program according to its
  major function.
Model building
_software.classification
Coot
  The classification of the program according to its
  major function.
Refinement
_software.classification
PHENIX (1.10)
  The classification of the program according to its
  major function.
General information
Spacegroup name
_symmetry.space_group_name_H-M
H 3 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}
173.877
  Unit-cell length a corresponding to the structure reported in
  angstroms.
173.877
  Unit-cell length b corresponding to the structure reported in
  angstroms.
71.906
  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
0.97950
  The radiation wavelength in angstroms.
 Å

Data quality metricsOverallInnerShellOuterShell
Low resolution limit [Å]
_reflns.d_resolution_low _reflns_shell.d_res_low
52.000
  The largest value in angstroms for the interplanar spacings
  for the reflection data. This is called the lowest resolution.
52.000
  The highest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the lowest
  resolution.
2.300
  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
2.186
  The smallest value in angstroms for the interplanar spacings
  for the reflection data. This is called the highest resolution.
6.910
  The smallest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the highest
  resolution.
2.190
  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
0.039
  The R value for merging intensities satisfying the observed
  criteria in this data set.
0.017
  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
0.840
  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
0.041
  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.
0.018
  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.
0.890
  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
0.014
  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.
0.006
  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.
0.293
  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_shell.number_measured_all
-
6049
  The total number of reflections measured for this
  shell.
28703
  The total number of reflections measured for this
  shell.
Total number unique
_reflns.number_obs _reflns_shell.number_unique_obs
21590
  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.
728
  The total number of measured reflections classified as 'observed'
  (see _reflns.observed_criterion) which are symmetry-unique
  after merging for this shell.
3120
  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.pdbx_netI_over_sigmaI_obs
27.70
  The mean of the ratio of the intensities to their
  standard uncertainties, <I/sigma(I)>.
105.60
  The mean of the ratio of the intensities to their
  standard uncertainties of observed reflections
  (see _reflns.observed_criterion) in the resolution shell.
  
  _reflns_shell.pdbx_netI_over_sigmaI_obs = <I/sigma(I)>
2.50
  The mean of the ratio of the intensities to their
  standard uncertainties of observed reflections
  (see _reflns.observed_criterion) in the resolution shell.
  
  _reflns_shell.pdbx_netI_over_sigmaI_obs = <I/sigma(I)>
Completeness [%]
_reflns.percent_possible_obs _reflns_shell.percent_possible_all
100.0
  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.
99.7
  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
9.1
  Overall redundancy for this data set.
8.3
  Redundancy for the current shell.
9.2
  Redundancy for the current shell.
CC(1/2)
_reflns.pdbx_CC_half _reflns_shell.pdbx_CC_half
1.000
  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
1.000
  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
0.905
  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

Refinement
PDB entry ID
_entry.id
7NNB
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2021-02-24
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
44.6 - 2.186 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.1986 / 0.2595
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
2AP9