Data quality metrics extracted from 6zev.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 6ZEV at RCSB, PDBe, PDBj

Experiment
Method
_exptl.method
ELECTRON CRYSTALLOGRAPHY
  The method used in the experiment.
Software
Data reduction
_software.classification
DIALS (1.10)
  The classification of the program according to its
  major function.
Data scaling
_software.classification
Aimless (0.7.1)
  The classification of the program according to its
  major function.
Phasing
_software.classification
PHASER (2.8.2)
  The classification of the program according to its
  major function.
Refinement
_software.classification
REFMAC (5.8.0258)
  The classification of the program according to its
  major function.
General information
Spacegroup name
_symmetry.space_group_name_H-M
P 43 21 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}
67.328
  Unit-cell length a corresponding to the structure reported in
  angstroms.
67.328
  Unit-cell length b corresponding to the structure reported in
  angstroms.
106.599
  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.
90.0
  Unit-cell angle gamma of the reported structure in degrees.
Wavelength
_diffrn_radiation_wavelength.wavelength
NA

Data quality metricsOverallOuterShell
Low resolution limit [Å]
_reflns.d_resolution_low _reflns_shell.d_res_low
56.989
  The largest value in angstroms for the interplanar spacings
  for the reflection data. This is called the lowest resolution.
2.490
  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_shell.d_res_high
-
2.400
  The smallest value in angstroms for the interplanar spacings
  for the reflections in this shell. This is called the highest
  resolution.
  - -
Rmerge
_reflns_shell.Rmerge_I_obs
-
1.220
  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_shell.pdbx_Rrim_I_all
-
1.327
  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_shell.pdbx_Rpim_I_all
-
0.515
  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_obs
-
12723
  The number of reflections classified as 'observed'
  (see _reflns.observed_criterion) for this
  shell.
Total number unique
_reflns_shell.number_unique_obs
-
1035
  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_shell.meanI_over_sigI_obs
-
2.00
  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_shell.percent_possible_all
-
99.7
  The percentage of geometrically possible reflections represented
  by all reflections measured for this shell.
Multiplicity
_reflns_shell.pdbx_redundancy
-
12.3
  Redundancy for the current shell.
CC(1/2)
_reflns_shell.pdbx_CC_half
-
0.701
  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
6ZEV
Deposition date
_pdbx_database_status.recvd_initial_deposition_date
2020-06-16
Resolution
_refine.ls_d_res_low _refine.ls_d_res_high
57.0 - 2.400 Å
Rwork/Rfree
_refine.ls_R_factor_R_work _refine.ls_R_factor_R_free
0.1996 / 0.2427
Structure solution method
_refine.pdbx_method_to_determine_struct
MOLECULAR REPLACEMENT
Starting model (for MR)
_refine.pdbx_starting_model
2ID8