data_7UJZ

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7UJZ
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7UJZ
_pdbx_vrpt_summary.PDB_deposition_date         2022-03-31
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-08-16
_pdbx_vrpt_summary.report_creation_date        2023-08-07:21:05
_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  "MERCURY (II) ION"  
6  non-polymer  "CADMIUM ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
E  5  
F  6  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  3.94  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    6.33  141614     ?     ?  
2  2  1   33.30    1009  3.70  4.18  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1007  3.64  4.24  
5  1  3   27.11  130704     ?     ?  
6  2  3   86.81    1036  3.68  4.20  
#
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  1.21  0.91  481  741  
2  1  2  B  B  1.05  0.81  156  237  
3  1  3  C  C  1.07  0.69  160  245  
4  1  4  D  D  1.20  1.06  161  245  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       23.93
_pdbx_vrpt_summary_geometry.num_H_reduce     477
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   958
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.89
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1468
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.16
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            354.937
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         227.713
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.27(4.00A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2361
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.161
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.479
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.306
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.906
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.058
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.25
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.94
_pdbx_vrpt_summary_diffraction.EDS_res_low               53.04
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[227.687,227.687,176.845,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.241
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 7.10% 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         1
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         61.53
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      130
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.51
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.94
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        41.07
_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     3  ?     
 3  1  1  A   3  DG  A    3  .  ?        ?     ?     3  ?     
 4  1  1  A   4  DC  A    4  .  ?        ?     ?     2  ?     
 5  1  1  A   5  DA  A    5  .  ?        ?     ?     2  ?     
 6  1  1  A   6  DG  A    6  .  ?        ?     ?     1  ?     
 7  1  1  A   7  DC  A    7  .  ?        ?     ?     ?  ?     
 8  1  1  A   8  DC  A    8  .  ?        ?     ?     5  ?     
 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  DT  A   12  .  ?        ?     ?     5  ?     
13  1  1  A  13  DT  A   13  .  ?        ?     ?     3  ?     
14  1  1  A  14  DG  A   14  .  ?        ?     ?     2  ?     
15  1  1  A  15  DG  A   15  .  ?        ?     ?     1  ?     
16  1  1  A  16  DA  A   16  .  ?        ?     ?     ?  ?     
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  .  ?        ?     ?     1  ?     
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  .  ?        ?     ?     2  ?     
24  1  2  B   3  DA  B    3  .  ?        ?     ?     3  ?     
25  1  2  B   4  DT  B    4  .  ?        ?     ?     1  ?     
26  1  2  B   5  DA  B    5  .  ?        ?     ?     ?  ?     
27  1  2  B   6  DC  B    6  .  ?        ?     ?     ?  ?     
28  1  2  B   7  DA  B    7  .  ?        ?     ?     ?  ?     
29  1  3  C   1  DG  C    8  .  ?        ?     ?     2  ?     
30  1  3  C   2  DG  C    9  .  ?        ?     ?     ?  ?     
31  1  3  C   3  DC  C   10  .  ?        ?     ?     ?  ?     
32  1  3  C   4  DT  C   11  .  ?        ?     ?     1  ?     
33  1  3  C   5  DG  C   12  .  ?        ?     ?     1  ?     
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  .  ?        ?     ?     4  ?     
38  1  4  D   3  DG  D    3  .  ?        ?     ?     4  ?     
39  1  4  D   4  DA  D    4  .  ?        ?     ?     1  ?     
40  1  4  D   5  DT  D    5  .  ?        ?     ?     4  ?     
41  1  4  D   6  DG  D    6  .  ?        ?     ?     1  ?     
42  1  4  D   7  DT  D    7  .  ?        ?     ?     2  ?     
43  1  5  E   .  HG  B  101  .  ?        ?     ?     ?  Y     
44  1  6  F   .  CD  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  333.360    22  0.95    35  0.84  molprobity  1.000  
 2   2    11  328.720    24  0.84    37  1.52  molprobity  1.000  
 3   3    11  341.150    25  0.98    39  1.07  molprobity  1.000  
 4   4    11  350.230    21  1.14    32  1.01  molprobity  1.000  
 5   5    11  405.560    24  0.52    37  0.51  molprobity  1.000  
 6   6    11  404.450    25  0.46    39  0.65  molprobity  1.000  
 7   7    11  347.410    21  0.84    32  1.26  molprobity  1.000  
 8   8    11  346.700    21  0.99    32  1.30  molprobity  1.000  
 9   9    12  356.130    22  0.96    34  1.45  molprobity  1.000  
10  10    11  288.840    25  0.91    39  1.23  molprobity  1.000  
11  11    12  253.740    22  1.19    34  2.28  molprobity  1.000  
12  12    12  231.290    22  1.66    34  1.85  molprobity  1.000  
13  13    12  228.300    22  1.05    34  1.35  molprobity  1.000  
14  14    11  274.800    25  0.95    39  1.04  molprobity  1.000  
15  15    11  265.940    25  0.85    39  1.48  molprobity  1.000  
16  16    11  293.920    24  0.76    37  0.78  molprobity  1.000  
17  17    11  282.810    21  0.68    32  0.78  molprobity  1.000  
18  18    11  309.650    24  0.50    37  0.68  molprobity  1.000  
19  19    12  314.550    22  0.75    34  1.43  molprobity  1.000  
20  20    11  278.190    21  0.70    32  0.75  molprobity  1.000  
21  21    12  262.950    23  0.68    33  0.69  molprobity  1.000  
22  22    11  273.860    21  0.82    32  0.87  molprobity  1.000  
23  23    11  261.090    21  0.59    32  0.80  molprobity  1.000  
24  24    11  230.880    24  0.77    37  0.78  molprobity  1.000  
25  25    11  255.930    22  1.08    34  1.63  molprobity  1.000  
26  26    11  285.000    24  0.60    37  0.68  molprobity  1.000  
27  27    11  278.860    21  0.66    32  0.98  molprobity  1.000  
28  28    12  255.650    23  1.00    33  1.30  molprobity  1.000  
29  29    11  300.130    25  0.78    39  0.88  molprobity  1.000  
30  30    11  304.650    25  0.84    39  1.16  molprobity  1.000  
31  31    11  344.070    21  0.66    32  0.94  molprobity  1.000  
32  32    12  322.340    22  0.64    34  1.28  molprobity  1.000  
33  33    11  337.030    25  0.49    39  0.80  molprobity  1.000  
34  34    11  374.860    21  0.68    32  0.79  molprobity  1.000  
35  35    13  341.690    21  0.67    30  1.51  molprobity  1.000  
36  36    11  364.800    22  2.38    32  1.21  molprobity  1.000  
37  37    12  341.320    22  0.84    34  1.49  molprobity  1.000  
38  38    11  319.200    25  0.58    39  1.23  molprobity  1.000  
39  39    11  311.600    24  0.56    37  0.68  molprobity  1.000  
40  40    12  292.410    22  0.50    34  1.33  molprobity  1.000  
41  41    11  231.250    25  0.63    39  0.81  molprobity  1.000  
42  42    13  229.460    21  0.67    30  1.52  molprobity  1.000  
43  43     ?  154.520     ?     ?     ?     ?  ?           0.430  
44  44     ?  151.890     ?     ?     ?     ?  ?           0.810  
#
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   2  "H1'"    2  0.51  2.10  
 4   2  "H2''"   3  0.47  1.79  
 5   3  "H2''"   4  0.62  2.00  
 6   3  OP2      2  0.51  2.10  
 7   3  H8       3  0.47  1.79  
 8   4  "H2'"    5  0.66  2.30  
 9   4  "O5'"    4  0.62  2.00  
10   5  C8       5  0.66  2.30  
11   5  C4       6  0.40  2.89  
12   6  N7       6  0.40  2.89  
13   8  "H5''"   7  0.56  1.70  
14   8  "H5''"   8  0.44  2.51  
15   8  H6       7  0.56  1.70  
16   8  "H2'"    9  0.45  2.51  
17   8  C6       8  0.44  2.51  
18   9  "H2'"   10  0.63  2.33  
19   9  C6       9  0.45  2.51  
20  10  "H2'"   11  0.64  2.32  
21  10  C8      10  0.63  2.33  
22  11  C6      11  0.64  2.32  
23  11  "H2''"  12  0.53  2.08  
24  12  OP1     12  0.53  2.08  
25  12  "H2''"  13  0.51  2.11  
26  12  "H2'"   14  0.51  1.93  
27  12  "O4'"   15  0.44  2.75  
28  12  P       15  0.44  2.75  
29  13  "O5'"   13  0.51  2.11  
30  13  H71     14  0.51  1.93  
31  13  "O3'"   16  0.40  2.74  
32  14  "H2''"  17  0.48  2.49  
33  14  C8      16  0.40  2.74  
34  15  C8      17  0.48  2.49  
35  20  "H2''"  18  0.49  1.94  
36  21  "H5''"  18  0.49  1.94  
37  22  "H1'"   19  0.44  2.00  
38  23  "H2''"  20  0.50  2.45  
39  23  "H2''"  21  0.42  2.35  
40  24  C8      20  0.50  2.45  
41  24  "H2''"  22  0.50  2.10  
42  24  N7      21  0.42  2.35  
43  25  OP2     22  0.50  2.10  
44  29  "H2'"   23  0.47  2.29  
45  29  N3      23  0.47  2.29  
46  32  "H2''"  24  0.45  2.15  
47  33  OP1     24  0.45  2.15  
48  36  "H1'"   25  0.41  2.21  
49  37  "H2'"   26  0.72  2.24  
50  37  "H2'"   27  0.61  1.65  
51  37  "H2''"  28  0.46  2.15  
52  37  OP2     25  0.41  2.21  
53  38  C8      26  0.72  2.24  
54  38  H8      27  0.61  1.65  
55  38  "O5'"   28  0.46  2.15  
56  38  "H1'"   29  0.41  2.55  
57  39  C8      29  0.41  2.55  
58  40  C6      30  0.46  2.51  
59  40  "H5'"   30  0.46  2.51  
60  40  "H5'"   31  0.45  1.81  
61  40  H6      31  0.45  1.81  
62  41  "H2''"  32  0.49  1.93  
63  42  "H5''"  32  0.49  1.93  
64  42  "H2'"   19  0.44  2.00  
#
_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          1.481
_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            -10.53
#
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  112.547  108.000  0.700  6.50  
2  11  "O4'"  "C1'"  N1  114.232  108.000  0.700  8.90  
3  35  N3     C4     O4  123.013  119.900  0.600  5.19  
#
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  0.926  0.111  -1.056  
 2   2  21  0.941  0.139  -0.804  
 3   3  22  0.930  0.088  -1.274  
 4   4  19  0.968  0.073  -1.424  
 5   5  21  0.950  0.075  -1.369  
 6   6  22  0.934  0.106  -1.103  
 7   7  19  0.965  0.079  -1.372  
 8   8  19  0.897  0.101  -1.179  
 9   9  20  0.867  0.125  -1.080  
10  10  22  0.904  0.156  -0.629  
11  11  20  0.913  0.199  -0.407  
12  12  20  0.917  0.134  -0.998  
13  13  20  0.903  0.154  -0.816  
14  14  22  0.923  0.180  -0.401  
15  15  22  0.955  0.138  -0.800  
16  16  21  0.822  0.159  -0.628  
17  17  19  0.843  0.116  -1.048  
18  18  21  0.869  0.160  -0.619  
19  19  20  0.941  0.283   0.358  
20  20  19  0.960  0.363   1.113  
21  21  21  0.969  0.244   0.123  
22  22  19  0.921  0.134  -0.891  
23  23  19  0.944  0.174  -0.541  
24  24  21  0.921  0.196  -0.301  
25  25  20  0.923  0.141  -0.934  
26  26  21  0.926  0.107  -1.086  
27  27  19  0.941  0.135  -0.882  
28  28  21  0.924  0.182  -0.425  
29  29  22  0.937  0.109  -1.075  
30  30  22  0.966  0.105  -1.113  
31  31  19  0.952  0.119  -1.022  
32  32  20  0.916  0.094  -1.362  
33  33  22  0.923  0.075  -1.398  
34  34  19  0.950  0.090  -1.276  
35  35  20  0.936  0.141  -0.934  
36  36  20  0.939  0.085  -1.319  
37  37  20  0.940  0.088  -1.417  
38  38  22  0.871  0.113  -1.037  
39  39  21  0.867  0.118  -0.989  
40  40  20  0.945  0.129  -1.044  
41  41  22  0.941  0.119  -0.980  
42  42  20  0.953  0.102  -1.289  
43  43   1  0.961  0.062       ?  
44  44   1  0.978  0.077       ?  
#
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  
##
