data_8DYK

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8DYK
#
_pdbx_vrpt_summary.entry_id                    8DYK
_pdbx_vrpt_summary.PDB_deposition_date         2022-08-04
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2023-08-02
_pdbx_vrpt_summary.report_creation_date        2023-07-25:18:00
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,mogul,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      "DNA (5'-D(*AP*AP*CP*CP*CP*C)-3')"  
2  non-polymer  "SILVER ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  2  
F  2  
G  2  
H  2  
I  2  
J  2  
K  2  
L  2  
M  2  
N  3  
O  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  2.1  x-ray  
#
_pdbx_vrpt_percentile_type.id    1
_pdbx_vrpt_percentile_type.type  all_atom_clashscore
#
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  80.04  141614     ?     ?  
2  2  1  82.08    5710  2.10  2.10  
#
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  0.82  0.54  169  255  
2  1  1  B  B  0.67  0.48  172  259  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       2.68
_pdbx_vrpt_summary_geometry.num_H_reduce     132
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   341
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.51
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  514
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.75
#
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
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A  1  DA   A    1  A  ?     ?     
 2  1  1  A  1  DA   A    1  B  ?     ?     
 3  1  1  A  2  DA   A    2  .  ?     ?     
 4  1  1  A  3  DC   A    3  .  ?     ?     
 5  1  1  A  4  DC   A    4  .  ?     ?     
 6  1  1  A  5  DC   A    5  .  ?     ?     
 7  1  1  A  6  DC   A    6  A  ?     ?     
 8  1  1  A  6  DC   A    6  B  ?     ?     
 9  1  1  B  1  DA   B    1  .  ?     ?     
10  1  1  B  2  DA   B    2  A  ?     ?     
11  1  1  B  2  DA   B    2  B  ?     ?     
12  1  1  B  3  DC   B    3  .  ?     ?     
13  1  1  B  4  DC   B    4  .  ?     ?     
14  1  1  B  5  DC   B    5  .  ?     ?     
15  1  1  B  6  DC   B    6  A  ?     ?     
16  1  1  B  6  DC   B    6  B  ?     ?     
17  1  2  C  .  AG   A  101  .  ?     Y     
18  1  2  D  .  AG   A  102  .  ?     Y     
19  1  2  E  .  AG   A  103  .  ?     Y     
20  1  2  F  .  AG   A  104  .  ?     Y     
21  1  2  G  .  AG   A  105  .  ?     Y     
22  1  2  H  .  AG   A  106  .  ?     Y     
23  1  2  I  .  AG   A  107  .  ?     Y     
24  1  2  J  .  AG   A  108  .  ?     Y     
25  1  2  K  .  AG   B  101  .  ?     Y     
26  1  2  L  .  AG   B  102  .  ?     Y     
27  1  2  M  .  AG   B  103  .  ?     Y     
28  1  3  N  .  HOH  A  201  .  ?     ?     
29  1  3  N  .  HOH  A  202  .  ?     ?     
30  1  3  N  .  HOH  A  203  .  ?     ?     
31  1  3  N  .  HOH  A  204  .  ?     ?     
32  1  3  N  .  HOH  A  205  .  ?     ?     
33  1  3  N  .  HOH  A  206  .  ?     ?     
34  1  3  N  .  HOH  A  207  .  ?     ?     
35  1  3  N  .  HOH  A  208  .  ?     ?     
36  1  3  N  .  HOH  A  209  .  ?     ?     
37  1  3  N  .  HOH  A  210  .  ?     ?     
38  1  3  N  .  HOH  A  211  .  ?     ?     
39  1  3  N  .  HOH  A  212  .  ?     ?     
40  1  3  N  .  HOH  A  213  .  ?     ?     
41  1  3  N  .  HOH  A  214  .  ?     ?     
42  1  3  N  .  HOH  A  215  .  ?     ?     
43  1  3  O  .  HOH  B  201  .  ?     ?     
44  1  3  O  .  HOH  B  202  .  ?     ?     
45  1  3  O  .  HOH  B  203  .  ?     ?     
46  1  3  O  .  HOH  B  204  .  ?     ?     
47  1  3  O  .  HOH  B  205  .  ?     ?     
48  1  3  O  .  HOH  B  206  .  ?     ?     
49  1  3  O  .  HOH  B  207  .  ?     ?     
50  1  3  O  .  HOH  B  208  .  ?     ?     
51  1  3  O  .  HOH  B  209  .  ?     ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_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
 1   1     ?  21  0.44  33  0.60  molprobity  
 2   2     ?  21  0.44  33  0.60  molprobity  
 3   3    10  24  0.45  37  0.62  molprobity  
 4   4    10  21  0.65  32  0.96  molprobity  
 5   5    11  21  0.65  32  1.15  molprobity  
 6   6    11  21  0.57  32  0.84  molprobity  
 7   7     ?  20  0.55  28  0.82  molprobity  
 8   8     ?  20  0.55  28  0.82  molprobity  
 9   9    12  21  0.41  33  0.44  molprobity  
10  10     ?  24  0.49  37  0.62  molprobity  
11  11     ?  24  0.49  37  0.62  molprobity  
12  12    11  21  0.51  32  0.84  molprobity  
13  13    11  21  0.50  32  0.72  molprobity  
14  14    11  21  0.54  32  0.80  molprobity  
15  15     ?  20  0.46  28  0.62  molprobity  
16  16     ?  20  0.46  28  0.62  molprobity  
#
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  mogul        unknown                                                               Y  
3  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
