data_8DXA

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8DXA
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8DXA
_pdbx_vrpt_summary.PDB_deposition_date         2022-08-02
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2023-08-30
_pdbx_vrpt_summary.report_creation_date        2023-08-19:16:05
_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*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')"  
2  polymer      "DNA (5'-D(P*CP*CP*AP*CP*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  "MERCURY (II) ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
E  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  4.21  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   11.74  141614     ?     ?  
2  2  1   42.98    1047  3.80  4.62  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1064  3.70  4.72  
5  1  3   19.18  130704     ?     ?  
6  2  3   83.64    1008  3.78  4.66  
#
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  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  1.14  0.78  480  739  
2  1  2  B  B  1.06  0.80  155  235  
3  1  3  C  C  1.00  0.62  160  245  
4  1  4  D  D  1.17  1.00  161  245  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       17.27
_pdbx_vrpt_summary_geometry.num_H_reduce     475
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.80
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1464
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.11
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            329.216
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         255.799
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.51(4.14A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2022
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.170
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.488
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.325
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.949
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.086
_pdbx_vrpt_summary_diffraction.DCC_R                     0.24
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.27
_pdbx_vrpt_summary_diffraction.EDS_R                     0.27
_pdbx_vrpt_summary_diffraction.EDS_res_high              4.21
_pdbx_vrpt_summary_diffraction.EDS_res_low               65.76
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[259.591,259.591,193.285,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.279
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 7.02% 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         60.33
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      107
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.29
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       4.21
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        32.88
_pdbx_vrpt_summary_diffraction.PDB_R                     0.23
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.26
#
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     1  ?     
 3  1  1  A   3  DG  A    3  .  ?        ?     ?     1  ?     
 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  .  ?        ?     ?     2  ?     
10  1  1  A  10  DG  A   10  .  ?        ?     ?     2  ?     
11  1  1  A  11  DT  A   11  .  ?        ?     1     2  ?     
12  1  1  A  12  DC  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  .  ?        ?     ?     3  ?     
16  1  1  A  16  DA  A   16  .  ?        ?     ?     2  ?     
17  1  1  A  17  DC  A   17  .  ?        ?     ?     ?  ?     
18  1  1  A  18  DA  A   18  .  ?        ?     ?     ?  ?     
19  1  1  A  19  DT  A   19  .  ?        ?     ?     ?  ?     
20  1  1  A  20  DC  A   20  .  ?        ?     ?     ?  ?     
21  1  1  A  21  DA  A   21  .  ?        ?     ?     ?  ?     
22  1  2  B   1  DC  B    1  .  ?        ?     ?     ?  ?     
23  1  2  B   2  DC  B    2  .  ?        ?     ?     1  ?     
24  1  2  B   3  DA  B    3  .  ?        ?     ?     2  ?     
25  1  2  B   4  DC  B    4  .  ?        ?     ?     2  ?     
26  1  2  B   5  DA  B    5  .  ?        ?     ?     2  ?     
27  1  2  B   6  DC  B    6  .  ?        ?     ?     1  ?     
28  1  2  B   7  DA  B    7  .  ?        ?     1     ?  ?     
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  .  ?        ?     1     ?  ?     
36  1  4  D   1  DC  D    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  .  ?        ?     ?     ?  ?     
41  1  4  D   6  DG  D    6  .  ?        ?     ?     1  ?     
42  1  4  D   7  DT  D    7  .  ?        ?     ?     1  ?     
43  1  5  E   .  HG  B  101  .  ?        ?     ?     ?  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  417.460    22  0.75    35  1.03  molprobity  1.000  
 2   2    11  430.540    24  0.83    37  1.53  molprobity  1.000  
 3   3    11  467.730    25  0.88    39  0.95  molprobity  1.000  
 4   4    11  481.410    21  0.95    32  1.10  molprobity  1.000  
 5   5    11  518.960    24  0.65    37  0.50  molprobity  1.000  
 6   6    11  566.820    25  0.41    39  0.71  molprobity  1.000  
 7   7    11  484.440    21  0.80    32  1.32  molprobity  1.000  
 8   8    11  492.820    21  0.87    32  1.36  molprobity  1.000  
 9   9    12  528.510    22  0.97    34  1.48  molprobity  1.000  
10  10    11  395.550    25  0.70    39  1.20  molprobity  1.000  
11  11    12  348.570    22  0.90    34  1.90  molprobity  1.000  
12  12    11  306.580    21  1.07    32  1.18  molprobity  1.000  
13  13    12  347.470    22  0.63    34  1.16  molprobity  1.000  
14  14    11  400.280    25  1.05    39  1.03  molprobity  1.000  
15  15    11  366.860    25  0.82    39  1.37  molprobity  1.000  
16  16    11  372.650    24  0.77    37  0.76  molprobity  1.000  
17  17    11  366.120    21  0.56    32  0.94  molprobity  1.000  
18  18    11  382.210    24  0.51    37  0.73  molprobity  1.000  
19  19    12  363.830    22  0.70    34  1.37  molprobity  1.000  
20  20    11  363.010    21  0.63    32  0.78  molprobity  1.000  
21  21    12  331.160    23  0.46    33  0.74  molprobity  1.000  
22  22    11  353.540    21  0.87    32  1.04  molprobity  1.000  
23  23    11  315.180    21  0.71    32  0.79  molprobity  1.000  
24  24    11  262.760    24  0.73    37  1.03  molprobity  1.000  
25  25    10  244.630    21  0.82    32  1.00  molprobity  1.000  
26  26    11  329.830    24  0.56    37  0.60  molprobity  1.000  
27  27    11  340.750    21  0.71    32  1.06  molprobity  1.000  
28  28    12  335.860    23  1.09    33  1.64  molprobity  1.000  
29  29    11  328.130    25  0.72    39  0.77  molprobity  1.000  
30  30    11  355.910    25  0.58    39  0.77  molprobity  1.000  
31  31    11  353.790    21  0.70    32  0.89  molprobity  1.000  
32  32    12  385.100    22  0.45    34  1.29  molprobity  1.000  
33  33    11  437.100    25  0.51    39  0.75  molprobity  1.000  
34  34    11  461.270    21  0.61    32  0.84  molprobity  1.000  
35  35    13  478.260    21  0.73    30  1.54  molprobity  1.000  
36  36    11  416.620    22  2.27    32  1.21  molprobity  1.000  
37  37    12  388.690    22  0.80    34  1.40  molprobity  1.000  
38  38    11  366.370    25  0.66    39  1.47  molprobity  1.000  
39  39    11  365.410    24  0.58    37  0.64  molprobity  1.000  
40  40    12  371.180    22  0.38    34  1.27  molprobity  1.000  
41  41    11  297.630    25  0.57    39  0.64  molprobity  1.000  
42  42    13  308.590    21  0.41    30  1.35  molprobity  1.000  
43  43     ?  290.080     ?     ?     ?     ?  ?           0.210  
#
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  0.47  2.49  
 2   2  C8       1  0.47  2.49  
 3   3  "H2''"   2  0.56  2.05  
 4   4  "H2'"    3  0.77  2.19  
 5   4  "O5'"    2  0.56  2.05  
 6   5  C8       3  0.77  2.19  
 7   8  "H5''"   4  0.49  1.77  
 8   8  H6       4  0.49  1.77  
 9   8  "H2'"    5  0.46  2.50  
10   9  "H2'"    6  0.81  2.16  
11   9  C6       5  0.46  2.50  
12  10  C8       6  0.81  2.16  
13  10  "H2'"    7  0.68  2.29  
14  11  C6       7  0.68  2.29  
15  11  "H2''"   8  0.45  2.16  
16  12  OP1      8  0.45  2.16  
17  12  "H2''"   9  0.43  2.18  
18  12  P       10  0.42  2.77  
19  12  "O4'"   10  0.42  2.77  
20  13  "O5'"    9  0.43  2.18  
21  14  "H2''"  11  0.55  2.41  
22  15  C8      11  0.55  2.41  
23  15  "H4'"   12  0.44  2.17  
24  15  "H2''"  13  0.43  2.18  
25  16  OP1     12  0.44  2.17  
26  16  "O5'"   13  0.43  2.18  
27  23  "H2''"  14  0.43  2.54  
28  24  "H2''"  15  0.47  2.14  
29  24  C8      14  0.43  2.54  
30  25  "H2''"  16  0.53  2.43  
31  25  OP2     15  0.47  2.14  
32  26  C8      16  0.53  2.43  
33  26  "H2''"  17  0.43  2.52  
34  27  C6      17  0.43  2.52  
35  32  "H2'"   18  0.57  2.39  
36  32  "H2''"  19  0.42  2.19  
37  33  C8      18  0.57  2.39  
38  33  OP1     19  0.42  2.19  
39  36  "H1'"   20  0.45  2.16  
40  37  "H2'"   21  0.48  2.48  
41  37  OP2     20  0.45  2.16  
42  37  "H2''"  22  0.45  2.15  
43  38  C8      21  0.48  2.48  
44  38  "O5'"   22  0.45  2.15  
45  41  "H2''"  23  0.46  1.97  
46  42  "H5''"  23  0.46  1.97  
#
_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          1.485
_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            -10.19
#
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  112.686  108.000  0.700  6.70  
2  11  "O4'"  "C1'"  N1  112.771  108.000  0.700  6.82  
3  28  "O4'"  "C1'"  N9  111.887  108.000  0.700  5.55  
4  35  N3     C4     O4  123.130  119.900  0.600  5.38  
5  38  "O4'"  "C1'"  N9  111.583  108.000  0.700  5.12  
#
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  0.946  0.082  -1.179  
 2   2  21  0.872  0.105  -1.089  
 3   3  22  0.890  0.089  -1.124  
 4   4  19  0.940  0.066  -1.291  
 5   5  21  0.935  0.084  -1.275  
 6   6  22  0.915  0.134  -0.769  
 7   7  19  0.866  0.109  -0.968  
 8   8  19  0.911  0.100  -1.036  
 9   9  20  0.840  0.109  -1.192  
10  10  22  0.921  0.134  -0.769  
11  11  20  0.848  0.167  -0.697  
12  12  19  0.756  0.211  -0.203  
13  13  20  0.902  0.216  -0.278  
14  14  22  0.920  0.121  -0.872  
15  15  22  0.966  0.055  -1.392  
16  16  21  0.978  0.043  -1.637  
17  17  19  0.952  0.058  -1.351  
18  18  21  0.964  0.050  -1.575  
19  19  20  0.956  0.067  -1.551  
20  20  19  0.937  0.087  -1.134  
21  21  21  0.947  0.095  -1.178  
22  22  19  0.884  0.117  -0.908  
23  23  19  0.872  0.107  -0.983  
24  24  21  0.924  0.116  -0.992  
25  25  19  0.825  0.130  -0.811  
26  26  21  0.882  0.116  -0.992  
27  27  19  0.916  0.085  -1.149  
28  28  21  0.865  0.100  -1.133  
29  29  22  0.929  0.079  -1.203  
30  30  22  0.947  0.088  -1.132  
31  31  19  0.964  0.065  -1.299  
32  32  20  0.940  0.140  -0.927  
33  33  22  0.916  0.171  -0.478  
34  34  19  0.953  0.095  -1.074  
35  35  20  0.953  0.112  -1.167  
36  36  20  0.956  0.087  -1.134  
37  37  20  0.977  0.052  -1.679  
38  38  22  0.954  0.074  -1.242  
39  39  21  0.980  0.052  -1.557  
40  40  20  0.957  0.068  -1.542  
41  41  22  0.966  0.064  -1.321  
42  42  20  0.950  0.079  -1.448  
43  43   1  0.883  0.382       ?  
#
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          2.35                                                                  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  
##
