data_8DAH

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8DAH
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8DAH
_pdbx_vrpt_summary.PDB_deposition_date         2022-06-13
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-25
_pdbx_vrpt_summary.report_creation_date        2023-10-14:23:10
_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  "DNA (5'-D(*GP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')"  
2  polymer  "DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')"  
3  polymer  "DNA (5'-D(P*GP*GP*CP*TP*GP*C)-3')"  
4  polymer  "DNA (5'-D(*CP*TP*GP*AP*TP*GP*T)-3')"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  5.47  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore  
2  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   5.02  141614     ?     ?  
2  2  1  28.70    1007  3.90  7.04  
3  1  2  84.49  130704     ?     ?  
4  2  2  99.69    1019  3.82  7.12  
#
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  0.98  0.67  458  705  
2  1  2  B  B  0.95  0.64  157  239  
3  1  3  C  C  1.01  0.57  138  211  
4  1  4  D  D  1.16  0.65  157  241  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       26.81
_pdbx_vrpt_summary_geometry.num_H_reduce     454
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   910
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.65
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1396
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.01
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            -10.000
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         274.423
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.13(5.40A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1396
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.063
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.447
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.275
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.742
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.129
_pdbx_vrpt_summary_diffraction.DCC_R                     0.15
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.20
_pdbx_vrpt_summary_diffraction.EDS_R                     0.22
_pdbx_vrpt_summary_diffraction.EDS_res_high              5.47
_pdbx_vrpt_summary_diffraction.EDS_res_low               61.30
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[278.534,278.534,459.726,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.535
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 5.74% of the height of the origin peak. No significant pseudotranslation is detected."
_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         71.70
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      71
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.09
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       5.47
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        40.13
_pdbx_vrpt_summary_diffraction.PDB_R                     0.15
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.20
#
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.count_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_symm_clashes
 1  1  1  A   1  DG  A  102  .  ?        ?     1     1  
 2  1  1  A   2  DG  A  103  .  ?        ?     1     ?  
 3  1  1  A   3  DC  A  104  .  ?        ?     1     ?  
 4  1  1  A   4  DA  A  105  .  ?        ?     1     ?  
 5  1  1  A   5  DG  A  106  .  ?        ?     ?     ?  
 6  1  1  A   6  DC  A  107  .  ?        ?     2     ?  
 7  1  1  A   7  DC  A  108  .  ?        ?     6     ?  
 8  1  1  A   8  DT  A  109  .  ?        ?     1     ?  
 9  1  1  A   9  DG  A  110  .  ?        ?     2     ?  
10  1  1  A  10  DT  A  111  .  ?        1     2     ?  
11  1  1  A  11  DA  A  112  .  ?        ?     2     ?  
12  1  1  A  12  DC  A  113  .  ?        ?     2     ?  
13  1  1  A  13  DG  A  114  .  ?        ?     1     ?  
14  1  1  A  14  DG  A  115  .  ?        ?     4     ?  
15  1  1  A  15  DA  A  116  .  ?        ?     4     ?  
16  1  1  A  16  DC  A  117  .  ?        ?     ?     ?  
17  1  1  A  17  DA  A  118  .  ?        ?     ?     ?  
18  1  1  A  18  DT  A  119  .  ?        ?     1     ?  
19  1  1  A  19  DC  A  120  .  ?        ?     1     ?  
20  1  1  A  20  DA  A  121  .  ?        ?     ?     ?  
21  1  2  B   1  DC  B  119  .  ?        ?     3     ?  
22  1  2  B   2  DC  B  120  .  ?        ?     2     ?  
23  1  2  B   3  DG  B  121  .  ?        ?     ?     ?  
24  1  2  B   4  DT  B  122  .  ?        ?     1     ?  
25  1  2  B   5  DA  B  123  .  ?        ?     1     ?  
26  1  2  B   6  DC  B  124  .  ?        ?     3     ?  
27  1  2  B   7  DA  B  125  .  ?        ?     4     ?  
28  1  3  C   1  DG  C  209  .  ?        ?     6     ?  
29  1  3  C   2  DG  C  210  .  ?        ?     4     ?  
30  1  3  C   3  DC  C  211  .  ?        ?     4     ?  
31  1  3  C   4  DT  C  212  .  ?        ?     3     ?  
32  1  3  C   5  DG  C  213  .  ?        ?     ?     ?  
33  1  3  C   6  DC  C  214  .  ?        ?     ?     ?  
34  1  4  D   1  DC  D  202  .  ?        ?     ?     1  
35  1  4  D   2  DT  D  203  .  ?        ?     ?     ?  
36  1  4  D   3  DG  D  204  .  ?        ?     ?     ?  
37  1  4  D   4  DA  D  205  .  ?        ?     ?     ?  
38  1  4  D   5  DT  D  206  .  ?        ?     ?     ?  
39  1  4  D   6  DG  D  207  .  ?        ?     1     ?  
40  1  4  D   7  DT  D  208  .  ?        ?     2     ?  
#
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  12  22  0.43  35  1.10  molprobity  
 2   2  11  25  0.74  39  1.09  molprobity  
 3   3  11  21  0.88  32  1.15  molprobity  
 4   4  11  24  0.87  37  0.76  molprobity  
 5   5  11  25  0.55  39  0.86  molprobity  
 6   6  11  21  0.59  32  0.87  molprobity  
 7   7  11  21  0.51  32  0.74  molprobity  
 8   8  12  22  0.84  34  1.26  molprobity  
 9   9  11  25  0.42  39  0.64  molprobity  
10  10  12  22  0.63  34  1.33  molprobity  
11  11  11  24  0.73  37  1.07  molprobity  
12  12  11  21  0.57  32  0.60  molprobity  
13  13  11  25  0.42  39  0.78  molprobity  
14  14  11  25  0.73  39  1.15  molprobity  
15  15  11  24  0.87  37  0.72  molprobity  
16  16  11  21  0.71  32  1.33  molprobity  
17  17  11  24  0.65  37  0.81  molprobity  
18  18  12  22  0.85  34  1.31  molprobity  
19  19  11  21  0.62  32  0.80  molprobity  
20  20  12  23  0.52  33  0.65  molprobity  
21  21  11  21  0.76  32  1.15  molprobity  
22  22  11  21  0.50  32  0.96  molprobity  
23  23  11  25  0.66  39  0.82  molprobity  
24  24  12  22  0.56  34  1.31  molprobity  
25  25  11  24  0.60  37  0.68  molprobity  
26  26  11  21  0.72  32  0.98  molprobity  
27  27  12  23  0.66  33  0.64  molprobity  
28  28  11  25  0.56  39  0.80  molprobity  
29  29  11  25  0.52  39  0.77  molprobity  
30  30  11  21  0.68  32  1.41  molprobity  
31  31  12  22  0.63  34  1.29  molprobity  
32  32  11  25  0.53  39  0.74  molprobity  
33  33  12  20  0.52  28  0.99  molprobity  
34  34  12  18  0.71  28  1.14  molprobity  
35  35  12  22  0.60  34  1.43  molprobity  
36  36  11  25  0.63  39  0.58  molprobity  
37  37  11  24  0.63  37  1.04  molprobity  
38  38  12  22  0.63  34  1.19  molprobity  
39  39  11  25  0.69  39  1.28  molprobity  
40  40  13  21  0.69  30  1.36  molprobity  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
 1   1  "H2'"    1  0.53  2.43  
 2   2  C8       1  0.53  2.43  
 3   3  "H2''"   2  0.49  2.48  
 4   4  C8       2  0.49  2.48  
 5   6  O2       3  0.72  2.22  
 6   6  "H1'"    4  0.44  1.82  
 7   7  N4       3  0.72  2.22  
 8   7  N4       5  0.52  2.05  
 9   7  H42      6  0.69  1.38  
10   7  H42      7  0.53  1.57  
11   7  H42      8  0.45  2.09  
12   7  H5       4  0.44  1.82  
13   8  "H2'"    9  0.56  2.40  
14   9  C8       9  0.56  2.40  
15   9  "H2''"  10  0.52  1.92  
16  10  "H2''"  11  0.59  2.37  
17  10  "H5''"  10  0.52  1.92  
18  11  C8      11  0.59  2.37  
19  11  "H4'"   12  0.55  2.04  
20  12  OP1     12  0.55  2.04  
21  12  "H1'"   13  0.47  2.50  
22  13  C5      13  0.47  2.50  
23  14  "H1'"   14  0.63  2.34  
24  14  "H1'"   15  0.44  2.31  
25  14  N3      16  0.42  2.68  
26  14  N3      17  0.40  2.89  
27  15  C8      14  0.63  2.34  
28  15  N7      15  0.44  2.31  
29  15  N7      16  0.42  2.68  
30  15  C5      17  0.40  2.89  
31  18  "H2''"  18  0.42  2.19  
32  19  "O5'"   18  0.42  2.19  
33  21  "O4'"   19  0.50  2.12  
34  21  "H2'"   20  0.48  2.48  
35  21  "H2'"   21  0.41  2.55  
36  22  C6      20  0.48  2.48  
37  22  C5      21  0.41  2.55  
38  24  "H2''"  22  0.44  2.33  
39  25  N7      22  0.44  2.33  
40  26  "H2'"   23  0.47  2.49  
41  26  "C2'"   24  0.43  2.49  
42  26  "H2''"  25  0.40  2.02  
43  27  C8      23  0.47  2.49  
44  27  "H5'"   24  0.43  2.49  
45  27  "H5'"   25  0.40  2.02  
46  27  N3      26  0.41  2.35  
47  28  H22      6  0.69  1.38  
48  28  H22      5  0.52  2.05  
49  28  H1       7  0.53  1.57  
50  28  "H2'"   27  0.49  2.47  
51  28  N2       8  0.45  2.09  
52  28  "H1'"   26  0.41  2.35  
53  29  "H2'"   28  0.56  2.40  
54  29  C8      27  0.49  2.47  
55  29  "O5'"   29  0.47  1.96  
56  29  H8      29  0.47  1.96  
57  30  C6      28  0.56  2.40  
58  30  "H2'"   30  0.46  1.96  
59  30  "H2'"   31  0.42  2.49  
60  30  "H2'"   32  0.41  2.56  
61  31  H71     30  0.46  1.96  
62  31  C7      31  0.42  2.49  
63  31  C5      32  0.41  2.56  
64  39  "H2''"  33  0.44  2.17  
65  40  "H2'"   19  0.50  2.12  
66  40  "O4'"   33  0.44  2.17  
#
loop_
_pdbx_vrpt_instance_symm_clashes.ordinal
_pdbx_vrpt_instance_symm_clashes.instance_id
_pdbx_vrpt_instance_symm_clashes.label_atom_id
_pdbx_vrpt_instance_symm_clashes.scid
_pdbx_vrpt_instance_symm_clashes.symop
_pdbx_vrpt_instance_symm_clashes.clashmag
_pdbx_vrpt_instance_symm_clashes.dist
1   1  N2  0  1_555  0.04  2.16  
2  34  O2  0  5_555  0.04  2.16  
#
_pdbx_vrpt_instance_intra_angle_outliers.ordinal      1
_pdbx_vrpt_instance_intra_angle_outliers.instance_id  10
_pdbx_vrpt_instance_intra_angle_outliers.atom_1       N3
_pdbx_vrpt_instance_intra_angle_outliers.atom_2       C4
_pdbx_vrpt_instance_intra_angle_outliers.atom_3       O4
_pdbx_vrpt_instance_intra_angle_outliers.obs          122.909
_pdbx_vrpt_instance_intra_angle_outliers.mean         119.900
_pdbx_vrpt_instance_intra_angle_outliers.stdev        0.600
_pdbx_vrpt_instance_intra_angle_outliers.Z            5.02
#
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          2.36                                                                  Y  
3  dcc          '"2.27  (2023-04-10)"'                                                Y  
4  xtriage      1.13                                                                  Y  
5  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
