PDBx/mmCIF
A Member of the wwPDB

Data Category refine

Browse:

General

Category name
refine
Required in PDB entries
No
Category group membership
refine_group
Used in current PDB entries
Yes, in about 89.4 % of entries

Category Relationship Diagrams

70
View full category relationship diagram including all dictionary data categories
70
View abbreviated category relationship diagram including only those categories used in current PDB entries.

Category Description

Additional Descriptive Information for Depositors 

 
Enter the refinement parameters of the deposited structure.

Category Examples

2

View/hide Category Examples

Category Example1

View/Hide Category Example 
 
    _refine.entry_id                       '5HVP'
    _refine.pdbx_refine_id                'x-ray'
    _refine.ls_number_reflns_obs           12901
    _refine.ls_number_restraints           6609
    _refine.ls_number_parameters           7032
    _refine.ls_R_factor_obs                0.176
    _refine.ls_weighting_scheme            calc
    _refine.ls_weighting_details
    ; Sigdel model of Konnert-Hendrickson:
      Sigdel: Afsig +  Bfsig*(sin(theta)/lambda-1/6)
      Afsig = 22.0, Bfsig = -150.0 at the beginning of refinement.
      Afsig = 15.5, Bfsig =  -50.0 at the end of refinement.
    ;

Category Example2

View/Hide Category Example 
 
    _refine.entry_id                       'TOZ'
    _refine.pdbx_refine_id                'x-ray'
    _refine.details                    sfls:_F_calc_weight_full_matrix

    _refine.ls_structure_factor_coef   F
    _refine.ls_matrix_type             full
    _refine.ls_weighting_scheme        'calc w=1/(\s^2^(F)+0.0004F^2^)'
    _refine.ls_hydrogen_treatment      'refxyz except H332B noref'
    _refine.ls_extinction_method       Zachariasen
    _refine.ls_extinction_coef         3514(42)
    _refine.ls_extinction_expression
                'equ(22) p292 "Crystallographic Computing" (1970)'

    _refine.ls_abs_structure_details
    ;      The absolute configuration was assigned to agree with the known
           chirality at C3 arising from its precursor l-leucine.
    ;
    _refine.ls_abs_structure_Flack     0
    _refine.ls_number_reflns_obs       1408
    _refine.ls_number_parameters       272
    _refine.ls_number_restraints       0
    _refine.ls_number_constraints      0
    _refine.ls_R_factor_all               .038
    _refine.ls_R_factor_obs               .034
    _refine.ls_wR_factor_all              .044
    _refine.ls_wR_factor_obs              .042
    _refine.ls_goodness_of_fit_all       1.462
    _refine.ls_goodness_of_fit_obs       1.515
    _refine.ls_shift_over_esd_max         .535
    _refine.ls_shift_over_esd_mean        .044
    _refine.diff_density_min              -.108
    _refine.diff_density_max              .131

Additional Category Example for Depositors

View/hide Example 
 
     _refine.ls_R_factor_all                    0.193
     _refine.ls_R_factor_obs                    0.186
     _refine.ls_R_factor_R_work                 0.178
     _refine.ls_d_res_high                      2.8
     _refine.ls_d_res_low                       8.0
     _refine.ls_number_reflns_obs               9284
     _refine.ls_percent_reflns_obs              87.4
     _refine.ls_number_reflns_all               12894
     _refine.ls_R_factor_R_free                 0.201
     _refine.ndb_ls_sigma_F                     2.0
     _refine.ndb_ls_sigma_I                     1.5
     _refine.ndb_R_Free_selection_details       'RANDOM'
     _refine.ndb_stereochemistry_target_values  'Engh & Huber'

Key Data Items

Category Data Items

View/hide item list