data_6DKY

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.066
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6DKY
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6DKY
_pdbx_vrpt_summary.PDB_deposition_date         2018-05-31
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-11-20
_pdbx_vrpt_summary.report_creation_date        2024-11-09:18:43
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer  ILE-LEU-GLY-SER-ILE-ILE-LEU-GLY  
2  water    water                            
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  1.239  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
4  RSRZ_outliers_percent         
5  R_value_R_free                
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
 1  1  1   99.96  180529     ?     ?  
 2  2  1  100.00    1509  1.22  1.26  
 3  1  2  100.00  177936     ?     ?  
 4  2  2  100.00    1478  1.22  1.26  
 5  1  3  100.00  177891     ?     ?  
 6  2  3  100.00    1476  1.22  1.26  
 7  1  4  100.00  164620     ?     ?  
 8  2  4  100.00    1389  1.22  1.26  
 9  1  5   67.79  164625     ?     ?  
10  2  5   11.93    1389  1.22  1.26  
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
 1  3  2  A  1  1  A  100.00  
 2  4  2  A  1  1  A  100.00  
 3  5  3  A  1  1  A  100.00  
 4  6  3  A  1  1  A  100.00  
 5  7  4  A  1  1  A  100.00  
 6  8  4  A  1  1  A  100.00  
 7  3  2  B  1  1  B  100.00  
 8  4  2  B  1  1  B  100.00  
 9  5  3  B  1  1  B  100.00  
10  6  3  B  1  1  B  100.00  
11  7  4  B  1  1  B  100.00  
12  8  4  B  1  1  B  100.00  
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  A  0.85  1.12  53  70  
2  1  1  B  B  0.79  0.55  53  70  
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       0.00
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   130
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 106
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.88
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                140
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.82
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            37.218
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         7.199
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.05(1.24A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3334
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.366
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.458
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.295
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.951
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,l,k:0.035
_pdbx_vrpt_summary_diffraction.DCC_R                     0.2016
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.2178
_pdbx_vrpt_summary_diffraction.EDS_R                     0.2054
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.24
_pdbx_vrpt_summary_diffraction.EDS_res_low               16.79
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[5.332,11.726,6.433,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.817
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 67.73 % of the origin peak, indicating pseudo-translational symmetry.  The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 4.9089e-06. The detected translational NCS is most likely also responsible for the elevated intensity ratio.  See the relevant section of the logfile for more details."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         0
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         99.67
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      2998
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.05
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.24
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        16.79
_pdbx_vrpt_summary_diffraction.PDB_R                     0.1992
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.2226
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.003 (Gargrove)"
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
 1  1  1  A  1  ILE  A    6  .  ?     
 2  1  1  A  2  LEU  A    7  .  ?     
 3  1  1  A  3  GLY  A    8  .  ?     
 4  1  1  A  4  SER  A    1  .  ?     
 5  1  1  A  5  ILE  A    2  .  ?     
 6  1  1  A  6  ILE  A    3  .  ?     
 7  1  1  A  7  LEU  A    4  .  ?     
 8  1  1  A  8  GLY  A    5  .  ?     
 9  1  1  B  1  ILE  B    6  .  ?     
10  1  1  B  2  LEU  B    7  .  ?     
11  1  1  B  3  GLY  B    8  .  ?     
12  1  1  B  4  SER  B    1  .  ?     
13  1  1  B  5  ILE  B    2  .  ?     
14  1  1  B  6  ILE  B    3  .  ?     
15  1  1  B  7  LEU  B    4  .  ?     
16  1  1  B  8  GLY  B    5  .  ?     
17  1  2  C  .  HOH  A  101  .  ?     
18  1  2  D  .  HOH  B  101  .  ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.OWAB
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
_pdbx_vrpt_model_instance_geometry.average_occupancy
 1   1  pt         ?      ?  ?          10   7.700     8  0.39    11  0.72  molprobity  1.000  
 2   2  mt      55.8   27.6  Favored    11   8.040     8  0.39    11  0.80  molprobity  1.000  
 3   3  ?       73.2   19.1  Favored     3   7.100     4  0.97     5  0.43  molprobity  1.000  
 4   4  t     -111.4  133.0  Favored     5   7.250     6  1.20     8  0.99  molprobity  1.000  
 5   5  mt     -60.3  -40.9  Favored    11   9.790     8  1.84    11  1.03  molprobity  1.000  
 6   6  mt     -72.0  -44.7  Favored    11  11.890     8  1.30    11  0.50  molprobity  1.000  
 7   7  mt     -82.9  -21.9  Favored    11   8.730     8  1.01    11  1.11  molprobity  1.000  
 8   8  ?          ?      ?  ?           3   8.340     3  0.92     2  0.72  molprobity  1.000  
 9   9  pt         ?      ?  ?          10   8.040     8  0.52    11  0.69  molprobity  1.000  
10  10  mt      56.3   30.9  Favored    11   9.590     8  0.44    11  0.88  molprobity  1.000  
11  11  ?       67.1   26.4  Favored     3   7.540     4  0.47     5  0.65  molprobity  1.000  
12  12  t     -117.6  127.8  Favored     5   7.170     6  0.45     8  0.61  molprobity  1.000  
13  13  pt     -73.1  -17.7  Favored    11  10.150     8  0.81    11  1.27  molprobity  1.000  
14  14  mt     -74.6  -51.5  Favored    11  10.870     8  0.35    11  0.44  molprobity  1.000  
15  15  mt     -73.5  -28.2  Favored    11   8.510     8  0.42    11  0.68  molprobity  1.000  
16  16  ?          ?      ?  ?           3   7.790     3  0.91     2  0.38  molprobity  1.000  
17  17  ?          ?      ?  ?           ?  19.100     ?     ?     ?     ?  ?           1.000  
18  18  ?          ?      ?  ?           ?  21.210     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_model_instance_density.ordinal
_pdbx_vrpt_model_instance_density.instance_id
_pdbx_vrpt_model_instance_density.natoms_eds
_pdbx_vrpt_model_instance_density.RSRCC
_pdbx_vrpt_model_instance_density.RSR
_pdbx_vrpt_model_instance_density.RSRZ
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
 1   1  8  0.966  0.057  -0.012  0.854   75.000  
 2   2  8  0.969  0.056  -0.120  0.968  100.000  
 3   3  4  0.966  0.052  -0.082  0.961  100.000  
 4   4  6  0.980  0.043  -0.509  0.905   83.330  
 5   5  8  0.925  0.102   1.824  0.642   62.500  
 6   6  8  0.953  0.091   1.376  0.348   62.500  
 7   7  8  0.960  0.059  -0.004  0.903  100.000  
 8   8  4  0.967  0.047  -0.235  0.944  100.000  
 9   9  8  0.968  0.060   0.110  0.950  100.000  
10  10  8  0.962  0.060   0.035  0.966  100.000  
11  11  4  0.952  0.064   0.284  0.890   75.000  
12  12  6  0.983  0.036  -0.707  0.870   83.330  
13  13  8  0.942  0.085   1.131  0.759   50.000  
14  14  8  0.941  0.090   1.335  0.444   87.500  
15  15  8  0.966  0.053  -0.236  0.930  100.000  
16  16  4  0.968  0.049  -0.174  0.923  100.000  
17  17  1  0.821  0.275       ?  0.633    0.000  
18  18  1  0.856  0.158       ?  0.752    0.000  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  eds          3.0                                                                   Y  
3  dcc          '"2.27  (2023-04-10)"'                                                Y  
4  xtriage      1.20.1                                                                Y  
5  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
