data_8DXX

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8DXX
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8DXX
_pdbx_vrpt_summary.PDB_deposition_date         2022-08-03
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2023-08-09
_pdbx_vrpt_summary.report_creation_date        2023-07-31:21:05
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,buster-report,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   Y
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*TP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')"  
2  polymer      "DNA (5'-D(P*CP*CP*AP*TP*AP*CP*A)-3')"  
3  polymer      "DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')"  
4  polymer      "DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')"  
5  non-polymer  "GOLD ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
E  5  
F  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  4.07  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore    
2  RSRZ_outliers_percent  
3  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   8.85  141614     ?     ?  
2  2  1  36.64    1013  3.74  4.42  
3  1  2  58.51  127900     ?     ?  
4  2  2  49.21    1012  3.68  4.48  
5  1  3  57.97  130704     ?     ?  
6  2  3  97.90    1133  3.70  4.46  
#
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   30.17  
2  4  2  A  1  1  A   25.69  
3  3  2  B  1  2  B  100.00  
4  4  2  B  1  2  B  100.00  
5  3  2  C  1  3  C  100.00  
6  4  2  C  1  3  C  100.00  
7  3  2  D  1  4  D  100.00  
8  4  2  D  1  4  D  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  1.16  0.82  481  741  
2  1  2  B  B  1.00  0.69  156  237  
3  1  3  C  C  1.00  0.62  160  245  
4  1  4  D  D  1.22  1.04  161  245  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       20.21
_pdbx_vrpt_summary_geometry.num_H_reduce     476
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   958
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.82
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1468
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.12
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 400.000
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            35.227
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         242.633
_pdbx_vrpt_summary_diffraction.I_over_sigma              -0.05(4.13A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1993
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.112
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.116
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.474
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.303
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.908
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.056
_pdbx_vrpt_summary_diffraction.DCC_R                     0.21
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.23
_pdbx_vrpt_summary_diffraction.EDS_R                     0.25
_pdbx_vrpt_summary_diffraction.EDS_res_high              4.07
_pdbx_vrpt_summary_diffraction.EDS_res_low               41.32
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[239.474,239.474,126.583,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.559
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 6.82% 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         54.17
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      86
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.32
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     2.38
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       4.07
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        32.67
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.24
#
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_bond_outliers
_pdbx_vrpt_model_instance.count_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A   1  DG  A    1  .  ?        ?     ?     1  ?     
 2  1  1  A   2  DA  A    2  .  ?        ?     1     2  ?     
 3  1  1  A   3  DG  A    3  .  ?        ?     ?     2  ?     
 4  1  1  A   4  DC  A    4  .  ?        ?     ?     2  ?     
 5  1  1  A   5  DA  A    5  .  ?        ?     ?     1  ?     
 6  1  1  A   6  DG  A    6  .  ?        ?     ?     ?  ?     
 7  1  1  A   7  DC  A    7  .  ?        ?     ?     ?  ?     
 8  1  1  A   8  DC  A    8  .  ?        ?     ?     3  ?     
 9  1  1  A   9  DT  A    9  .  ?        ?     ?     4  ?     
10  1  1  A  10  DG  A   10  .  ?        ?     ?     2  ?     
11  1  1  A  11  DT  A   11  .  ?        ?     1     2  ?     
12  1  1  A  12  DT  A   12  .  ?        ?     ?     4  ?     
13  1  1  A  13  DT  A   13  .  ?        ?     ?     1  ?     
14  1  1  A  14  DG  A   14  .  ?        ?     ?     1  ?     
15  1  1  A  15  DG  A   15  .  ?        ?     ?     2  ?     
16  1  1  A  16  DA  A   16  .  ?        ?     ?     1  ?     
17  1  1  A  17  DC  A   17  .  ?        ?     ?     ?  ?     
18  1  1  A  18  DA  A   18  .  ?        ?     ?     ?  ?     
19  1  1  A  19  DT  A   19  .  ?        ?     ?     1  ?     
20  1  1  A  20  DC  A   20  .  ?        ?     ?     2  ?     
21  1  1  A  21  DA  A   21  .  ?        ?     ?     1  ?     
22  1  2  B   1  DC  B    1  .  ?        ?     ?     1  ?     
23  1  2  B   2  DC  B    2  .  ?        ?     ?     3  ?     
24  1  2  B   3  DA  B    3  .  ?        ?     ?     2  ?     
25  1  2  B   4  DT  B    4  .  ?        ?     ?     1  ?     
26  1  2  B   5  DA  B    5  .  ?        ?     ?     1  ?     
27  1  2  B   6  DC  B    6  .  ?        ?     ?     ?  ?     
28  1  2  B   7  DA  B    7  .  ?        ?     ?     ?  ?     
29  1  3  C   1  DG  C    8  .  ?        ?     ?     ?  ?     
30  1  3  C   2  DG  C    9  .  ?        ?     ?     ?  ?     
31  1  3  C   3  DC  C   10  .  ?        ?     ?     ?  ?     
32  1  3  C   4  DT  C   11  .  ?        ?     ?     2  ?     
33  1  3  C   5  DG  C   12  .  ?        ?     ?     2  ?     
34  1  3  C   6  DC  C   13  .  ?        ?     ?     ?  ?     
35  1  3  C   7  DT  C   14  .  ?        ?     ?     ?  ?     
36  1  4  D   1  DC  D    1  .  ?        1     1     1  ?     
37  1  4  D   2  DT  D    2  .  ?        ?     ?     3  ?     
38  1  4  D   3  DG  D    3  .  ?        ?     1     2  ?     
39  1  4  D   4  DA  D    4  .  ?        ?     ?     ?  ?     
40  1  4  D   5  DT  D    5  .  ?        ?     ?     2  ?     
41  1  4  D   6  DG  D    6  .  ?        ?     ?     ?  ?     
42  1  4  D   7  DT  D    7  .  ?        ?     ?     ?  ?     
43  1  5  E   .  AU  B  101  .  ?        ?     ?     ?  Y     
44  1  5  F   .  AU  B  102  .  ?        ?     ?     ?  Y     
#
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.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    12  211.860    22  0.87    35  0.82  molprobity  1.000  
 2   2    11  219.910    24  0.85    37  1.52  molprobity  1.000  
 3   3    11  222.720    25  0.93    39  0.98  molprobity  1.000  
 4   4    11  231.030    21  1.15    32  1.28  molprobity  1.000  
 5   5    11  234.830    24  0.69    37  0.56  molprobity  1.000  
 6   6    11  231.090    25  0.48    39  0.72  molprobity  1.000  
 7   7    11  225.740    21  0.85    32  1.34  molprobity  1.000  
 8   8    11  218.630    21  0.73    32  1.44  molprobity  1.000  
 9   9    12  217.500    22  1.13    34  1.61  molprobity  1.000  
10  10    11  208.620    25  0.93    39  1.21  molprobity  1.000  
11  11    12  200.850    22  0.84    34  1.89  molprobity  1.000  
12  12    11  195.730    22  1.22    34  1.55  molprobity  1.000  
13  13    12  193.400    22  0.61    34  1.12  molprobity  1.000  
14  14    11  186.950    25  0.82    39  0.86  molprobity  1.000  
15  15    11  183.430    25  0.88    39  1.29  molprobity  1.000  
16  16    11  182.070    24  0.76    37  0.68  molprobity  1.000  
17  17    11  180.670    21  0.53    32  0.82  molprobity  1.000  
18  18    11  183.920    24  0.52    37  0.75  molprobity  1.000  
19  19    12  190.360    22  0.73    34  1.35  molprobity  1.000  
20  20    11  191.120    21  0.67    32  0.81  molprobity  1.000  
21  21    12  197.490    23  0.62    33  0.63  molprobity  1.000  
22  22    11  178.950    21  0.73    32  1.05  molprobity  1.000  
23  23    11  177.810    21  0.64    32  0.79  molprobity  1.000  
24  24    11  179.690    24  0.72    37  0.93  molprobity  1.000  
25  25    11  195.520    22  0.59    34  1.46  molprobity  1.000  
26  26    11  199.350    24  0.48    37  0.65  molprobity  1.000  
27  27    11  191.040    21  0.85    32  0.99  molprobity  1.000  
28  28    12  191.510    23  0.79    33  0.92  molprobity  1.000  
29  29    11  195.420    25  0.84    39  0.76  molprobity  1.000  
30  30    11  204.490    25  0.44    39  0.79  molprobity  1.000  
31  31    11  220.280    21  0.76    32  1.04  molprobity  1.000  
32  32    12  223.930    22  0.42    34  1.30  molprobity  1.000  
33  33    11  225.990    25  0.50    39  0.78  molprobity  1.000  
34  34    11  226.700    21  0.60    32  0.81  molprobity  1.000  
35  35    13  223.210    21  0.68    30  1.43  molprobity  1.000  
36  36    11  225.890    22  2.36    32  1.33  molprobity  1.000  
37  37    12  209.230    22  0.74    34  1.37  molprobity  1.000  
38  38    11  198.860    25  0.83    39  1.55  molprobity  1.000  
39  39    11  192.860    24  0.57    37  0.78  molprobity  1.000  
40  40    12  189.540    22  0.46    34  1.28  molprobity  1.000  
41  41    11  176.250    25  0.45    39  0.63  molprobity  1.000  
42  42    13  172.630    21  0.46    30  1.41  molprobity  1.000  
43  43     ?  174.480     ?     ?     ?     ?  ?           0.200  
44  44     ?  197.280     ?     ?     ?     ?  ?           0.280  
#
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  0.48  2.49  
 2   2  C8       1  0.48  2.49  
 3   2  "H1'"    2  0.46  2.14  
 4   3  "H2''"   3  0.57  2.05  
 5   3  OP2      2  0.46  2.14  
 6   4  "H2'"    4  0.77  2.19  
 7   4  "O5'"    3  0.57  2.05  
 8   5  C8       4  0.77  2.19  
 9   8  "H2'"    5  0.47  2.45  
10   8  "H2'"    6  0.44  2.00  
11   8  "H2'"    7  0.41  2.55  
12   9  "H2'"    8  0.82  2.13  
13   9  C7       5  0.47  2.45  
14   9  H72      6  0.44  2.00  
15   9  C6       7  0.41  2.55  
16  10  C8       8  0.82  2.13  
17  10  "H2'"    9  0.61  2.36  
18  11  C6       9  0.61  2.36  
19  11  "H2''"  10  0.46  2.15  
20  12  "H2''"  11  0.51  2.09  
21  12  OP1     10  0.46  2.15  
22  12  "O4'"   12  0.44  2.75  
23  12  P       12  0.44  2.75  
24  13  "O5'"   11  0.51  2.09  
25  14  "H2''"  13  0.61  2.35  
26  15  C8      13  0.61  2.35  
27  15  "H4'"   14  0.44  2.16  
28  16  OP1     14  0.44  2.16  
29  19  "H2''"  15  0.42  2.18  
30  20  "H2''"  16  0.55  1.88  
31  20  "O5'"   15  0.42  2.18  
32  21  "H5''"  16  0.55  1.88  
33  22  "H2'"   17  0.45  2.51  
34  23  "H2''"  18  0.63  2.34  
35  23  "H2''"  19  0.56  2.21  
36  23  C5      17  0.45  2.51  
37  24  C8      18  0.63  2.34  
38  24  N7      19  0.56  2.21  
39  25  "H2''"  20  0.41  2.55  
40  26  C8      20  0.41  2.55  
41  32  "H2'"   21  0.55  2.42  
42  32  "H2''"  22  0.45  2.16  
43  33  C8      21  0.55  2.42  
44  33  OP1     22  0.45  2.16  
45  36  "H1'"   23  0.47  2.15  
46  37  "H2'"   24  0.57  2.39  
47  37  "H2''"  25  0.51  2.11  
48  37  OP2     23  0.47  2.15  
49  38  C8      24  0.57  2.39  
50  38  "O5'"   25  0.51  2.11  
51  40  H6      26  0.44  1.82  
52  40  "H5'"   26  0.44  1.82  
#
_pdbx_vrpt_instance_intra_bond_outliers.ordinal      1
_pdbx_vrpt_instance_intra_bond_outliers.instance_id  36
_pdbx_vrpt_instance_intra_bond_outliers.atom_1       OP3
_pdbx_vrpt_instance_intra_bond_outliers.atom_2       P
_pdbx_vrpt_instance_intra_bond_outliers.obs          1.482
_pdbx_vrpt_instance_intra_bond_outliers.mean         1.607
_pdbx_vrpt_instance_intra_bond_outliers.stdev        0.012
_pdbx_vrpt_instance_intra_bond_outliers.Z            -10.43
#
loop_
_pdbx_vrpt_instance_intra_angle_outliers.ordinal
_pdbx_vrpt_instance_intra_angle_outliers.instance_id
_pdbx_vrpt_instance_intra_angle_outliers.atom_1
_pdbx_vrpt_instance_intra_angle_outliers.atom_2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3
_pdbx_vrpt_instance_intra_angle_outliers.obs
_pdbx_vrpt_instance_intra_angle_outliers.mean
_pdbx_vrpt_instance_intra_angle_outliers.stdev
_pdbx_vrpt_instance_intra_angle_outliers.Z
1   2  "O4'"  "C1'"  N9  112.628  108.000  0.700  6.61  
2  11  "O4'"  "C1'"  N1  112.512  108.000  0.700  6.45  
3  36  "O4'"  "C1'"  N1  111.690  108.000  0.700  5.27  
4  38  "O4'"  "C1'"  N9  111.974  108.000  0.700  5.68  
#
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
 1   1  19  0.943  0.126  -0.832  
 2   2  21  0.978  0.087  -1.248  
 3   3  22  0.924  0.110  -0.958  
 4   4  19  0.922  0.112  -0.946  
 5   5  21  0.856  0.194  -0.303  
 6   6  22  0.881  0.175  -0.446  
 7   7  19  0.944  0.076  -1.216  
 8   8  19  0.937  0.093  -1.089  
 9   9  20  0.842  0.120  -1.098  
10  10  22  0.858  0.164  -0.533  
11  11  20  0.879  0.218  -0.261  
12  12  20  0.889  0.423   1.489  
13  13  20  0.909  0.483   2.002  
14  14  22  0.950  0.119  -0.887  
15  15  22  0.909  0.087  -1.139  
16  16  21  0.933  0.085  -1.266  
17  17  19  0.955  0.109  -0.968  
18  18  21  0.951  0.159  -0.612  
19  19  20  0.951  0.149  -0.851  
20  20  19  0.942  0.106  -0.991  
21  21  21  0.937  0.114  -1.010  
22  22  19  0.932  0.259   0.157  
23  23  19  0.901  0.212  -0.196  
24  24  21  0.953  0.134  -0.833  
25  25  20  0.878  0.210  -0.330  
26  26  21  0.917  0.333   0.925  
27  27  19  0.911  0.279   0.307  
28  28  21  0.944  0.300   0.633  
29  29  22  0.934  0.117  -0.903  
30  30  22  0.953  0.134  -0.769  
31  31  19  0.933  0.136  -0.766  
32  32  20  0.928  0.125  -1.056  
33  33  22  0.899  0.131  -0.793  
34  34  19  0.910  0.083  -1.164  
35  35  20  0.902  0.149  -0.851  
36  36  20  0.876  0.132  -0.796  
37  37  20  0.930  0.142  -0.910  
38  38  22  0.916  0.169  -0.493  
39  39  21  0.949  0.160  -0.603  
40  40  20  0.924  0.138  -0.944  
41  41  22  0.933  0.129  -0.809  
42  42  20  0.905  0.169  -0.680  
43  43   1  0.914  0.081       ?  
44  44   1  0.983  0.110       ?  
#
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  eds          2.34                                                                  Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
