data_1A84

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1A84
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   nmr
#
_pdbx_vrpt_summary.entry_id                    1A84
_pdbx_vrpt_summary.PDB_deposition_date         1998-04-02
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-04-10
_pdbx_vrpt_summary.report_creation_date        2024-04-02:14:34
_pdbx_vrpt_summary.attempted_validation_steps  mogul,molprobity,validation-pack,coreclust,chemicalshiftanalysis,percentiles,writepdf,writexml,writecif
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "DNA D(CCTCTG*G*TCTCC)"  
2  polymer      "DNA D(GGAGACCAGAGG)"  
3  non-polymer  Cisplatin  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  pdb    
2  nmr  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   2.72  158937  ?     ?     
2  2  1  14.10   12864  ?     ?     
#
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  2.13  1.63  260  398  
2  1  2  B  B  2.60  1.46  284  438  
#
_pdbx_vrpt_summary_geometry.ordinal                 1
_pdbx_vrpt_summary_geometry.clashscore              44.68
_pdbx_vrpt_summary_geometry.clashscore_full_length  47.31
_pdbx_vrpt_summary_geometry.num_H_reduce            272
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ          544
_pdbx_vrpt_summary_geometry.bonds_RMSZ              1.54
_pdbx_vrpt_summary_geometry.num_angles_RMSZ         836
_pdbx_vrpt_summary_geometry.angles_RMSZ             2.38
#
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.count_plane_outliers
 1  1  1  A   1  DC   A   1  .  ?        ?     1     ?     ?  
 2  1  1  A   2  DC   A   2  .  ?        ?     2     2     ?  
 3  1  1  A   3  DT   A   3  .  ?        1     3     4     ?  
 4  1  1  A   4  DC   A   4  .  ?        1     2     4     ?  
 5  1  1  A   5  DT   A   5  .  ?        1     4     3     ?  
 6  1  1  A   6  DG   A   6  .  ?        ?     ?     4     ?  
 7  1  1  A   7  DG   A   7  .  ?        ?     1     2     ?  
 8  1  1  A   8  DT   A   8  .  ?        1     1     ?     ?  
 9  1  1  A   9  DC   A   9  .  ?        ?     1     ?     1  
10  1  1  A  10  DT   A  10  .  ?        1     ?     3     ?  
11  1  1  A  11  DC   A  11  .  ?        ?     3     5     ?  
12  1  1  A  12  DC   A  12  .  ?        1     2     ?     ?  
13  1  2  B   1  DG   B  13  .  ?        1     4     ?     ?  
14  1  2  B   2  DG   B  14  .  ?        ?     3     5     ?  
15  1  2  B   3  DA   B  15  .  ?        1     4     7     ?  
16  1  2  B   4  DG   B  16  .  ?        ?     3     3     ?  
17  1  2  B   5  DA   B  17  .  ?        ?     3     2     ?  
18  1  2  B   6  DC   B  18  .  ?        ?     2     4     ?  
19  1  2  B   7  DC   B  19  .  ?        ?     1     7     ?  
20  1  2  B   8  DA   B  20  .  ?        ?     5     2     ?  
21  1  2  B   9  DG   B  21  .  ?        ?     3     1     ?  
22  1  2  B  10  DA   B  22  .  ?        ?     3     3     ?  
23  1  2  B  11  DG   B  23  .  ?        ?     3     5     ?  
24  1  2  B  12  DG   B  24  .  ?        ?     3     2     ?  
25  1  3  C   .  CPT  A  13  .  ?        ?     ?     ?     ?  
#
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  18  1.38    28  2.12  molprobity  
 2   2    11  21  0.90    32  2.19  molprobity  
 3   3    12  22  1.78    34  2.41  molprobity  
 4   4    11  21  1.73    32  2.12  molprobity  
 5   5    12  22  1.99    34  2.45  molprobity  
 6   6    11  25  1.41    39  1.78  molprobity  
 7   7    11  25  1.25    39  1.81  molprobity  
 8   8    12  22  2.32    34  2.13  molprobity  
 9   9    11  21  1.62    32  1.95  molprobity  
10  10    12  22  1.94    34  2.10  molprobity  
11  11    11  21  1.05    32  2.13  molprobity  
12  12    12  20  1.61    28  2.32  molprobity  
13  13    12  22  1.79    35  2.70  molprobity  
14  14    11  25  1.48    39  2.57  molprobity  
15  15    11  24  1.77    37  2.75  molprobity  
16  16    11  25  1.23    39  2.65  molprobity  
17  17    11  24  1.50    37  2.66  molprobity  
18  18    11  21  1.24    32  2.32  molprobity  
19  19    11  21  1.71    32  1.98  molprobity  
20  20    11  24  1.34    37  2.66  molprobity  
21  21    11  25  1.27    39  2.54  molprobity  
22  22    11  24  1.26    37  2.56  molprobity  
23  23    11  25  1.44    39  2.80  molprobity  
24  24    12  24  1.40    35  2.76  molprobity  
25  25     ?   0     ?     ?     ?  mogul       
#
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   2  "H2''"   1  0.56  2.00  
 2   2  "C2'"    2  0.41  2.68  
 3   3  "H2''"   3  0.75  1.82  
 4   3  OP2      1  0.56  2.00  
 5   3  OP2      2  0.41  2.68  
 6   3  "C2'"    4  0.53  2.56  
 7   4  "H1'"    5  0.86  1.71  
 8   4  OP2      3  0.75  1.82  
 9   4  OP2      4  0.53  2.56  
10   4  "C1'"    6  0.66  2.42  
11   5  OP1      5  0.86  1.71  
12   5  OP1      6  0.66  2.42  
13   5  "H2''"   7  0.67  1.89  
14   6  "O5'"    7  0.67  1.89  
15   6  N2       8  0.56  2.73  
16   6  N2       9  0.49  2.60  
17   6  C2      10  0.52  2.78  
18   7  OP1     11  0.52  2.03  
19   7  "H4'"   11  0.52  2.03  
20  10  "H2''"  12  0.84  1.69  
21  10  O2      13  0.44  2.70  
22  10  "C2'"   14  0.44  2.53  
23  11  OP2     12  0.84  1.69  
24  11  OP2     14  0.44  2.53  
25  11  OP2     15  0.44  2.71  
26  11  C2      13  0.44  2.70  
27  11  C6      15  0.44  2.71  
28  14  N2      16  0.77  2.53  
29  14  N2      17  0.67  2.43  
30  14  "H4'"   18  0.75  1.79  
31  14  C2      19  0.67  2.83  
32  14  C2      20  0.42  2.87  
33  15  "H4'"   21  0.95  1.58  
34  15  C2      16  0.77  2.53  
35  15  C2      19  0.67  2.83  
36  15  OP1     18  0.75  1.79  
37  15  N3      17  0.67  2.43  
38  15  N3      20  0.42  2.87  
39  15  "C4'"   22  0.51  2.47  
40  16  OP1     21  0.95  1.58  
41  16  OP1     22  0.51  2.47  
42  16  "H2''"  23  0.48  2.07  
43  17  "H2''"  24  0.53  2.04  
44  17  OP2     23  0.48  2.07  
45  18  "H2''"  25  0.82  1.74  
46  18  "H2''"  26  0.41  2.44  
47  18  "C2'"   27  0.57  2.52  
48  18  "O5'"   24  0.53  2.04  
49  19  "O5'"   25  0.82  1.74  
50  19  "O5'"   27  0.57  2.52  
51  19  C2       8  0.56  2.73  
52  19  "H2''"  28  0.53  2.03  
53  19  N3      10  0.52  2.78  
54  19  N3       9  0.49  2.60  
55  19  "C5'"   26  0.41  2.44  
56  20  "O5'"   28  0.53  2.03  
57  20  "H2''"  29  0.44  2.13  
58  21  OP2     29  0.44  2.13  
59  22  "H2''"  30  0.50  2.06  
60  22  "C2'"   31  0.45  2.64  
61  22  "H1'"   32  0.41  2.16  
62  23  "H2''"  33  0.86  1.69  
63  23  "O5'"   30  0.50  2.06  
64  23  "O5'"   31  0.45  2.64  
65  23  "O5'"   32  0.41  2.16  
66  23  "C2'"   34  0.49  2.52  
67  24  OP2     33  0.86  1.69  
68  24  OP2     34  0.49  2.52  
#
_pdbx_vrpt_instance_intra_plane_outliers.ordinal      1
_pdbx_vrpt_instance_intra_plane_outliers.instance_id  9
_pdbx_vrpt_instance_intra_plane_outliers.type         sidechain
_pdbx_vrpt_instance_intra_plane_outliers.plane_rmsd   0.08
#
loop_
_pdbx_vrpt_instance_intra_bond_outliers.ordinal
_pdbx_vrpt_instance_intra_bond_outliers.instance_id
_pdbx_vrpt_instance_intra_bond_outliers.atom_1
_pdbx_vrpt_instance_intra_bond_outliers.atom_2
_pdbx_vrpt_instance_intra_bond_outliers.obs
_pdbx_vrpt_instance_intra_bond_outliers.mean
_pdbx_vrpt_instance_intra_bond_outliers.stdev
_pdbx_vrpt_instance_intra_bond_outliers.Z
1   3  C5     C7     1.528  1.496  0.006  5.35  
2   4  "C2'"  "C1'"  1.572  1.519  0.010  5.27  
3   5  C5     C7     1.527  1.496  0.006  5.22  
4   8  C5     C7     1.531  1.496  0.006  5.81  
5  10  C5     C7     1.534  1.496  0.006  6.26  
6  12  "C5'"  "C4'"  1.571  1.509  0.011  5.63  
7  13  "C2'"  "C1'"  1.575  1.519  0.010  5.60  
8  15  "C2'"  "C1'"  1.575  1.519  0.010  5.59  
#
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   1  "C4'"  "C3'"  "C2'"  109.519  103.100  0.900   7.13  
 2   2  "C4'"  "C3'"  "C2'"  108.274  103.100  0.900   5.75  
 3   2  "O4'"  "C1'"  N1     112.291  108.000  0.700   6.13  
 4   3  "C4'"  "C3'"  "C2'"  107.886  103.100  0.900   5.32  
 5   3  C4     C5     C6     121.249  118.000  0.600   5.41  
 6   3  C6     C5     C7     119.035  122.900  0.600  -6.44  
 7   4  "C4'"  "C3'"  "C2'"  108.013  103.100  0.900   5.46  
 8   4  "O4'"  "C1'"  N1     111.657  108.000  0.700   5.22  
 9   5  "C4'"  "C3'"  "C2'"  108.904  103.100  0.900   6.45  
10   5  C4     C5     C6     121.316  118.000  0.600   5.53  
11   5  C6     C5     C7     119.419  122.900  0.600  -5.80  
12   5  "O4'"  "C1'"  "C2'"  110.685  105.900  0.800   5.98  
13   7  "C4'"  "C3'"  "C2'"  108.441  103.100  0.900   5.93  
14   8  C4     C5     C6     121.143  118.000  0.600   5.24  
15   9  "C4'"  "C3'"  "C2'"  108.463  103.100  0.900   5.96  
16  11  "C4'"  "C3'"  "C2'"  108.794  103.100  0.900   6.33  
17  11  "O4'"  "C1'"  "C2'"  110.016  105.900  0.800   5.15  
18  11  "O4'"  "C1'"  N1     111.806  108.000  0.700   5.44  
19  12  "C4'"  "C3'"  "C2'"  109.491  103.100  0.900   7.10  
20  12  "O4'"  "C1'"  "C2'"  110.013  105.900  0.800   5.14  
21  13  "C4'"  "C3'"  "C2'"  109.216  103.100  0.900   6.79  
22  13  C5     N7     C8     101.707  104.300  0.500  -5.19  
23  13  C8     N9     C4     103.736  106.400  0.400  -6.66  
24  13  N7     C8     N9     117.791  113.100  0.500   9.38  
25  14  "C4'"  "C3'"  "C2'"  108.505  103.100  0.900   6.01  
26  14  C8     N9     C4     103.415  106.400  0.400  -7.46  
27  14  N7     C8     N9     117.467  113.100  0.500   8.73  
28  15  "C4'"  "C3'"  "C2'"  108.299  103.100  0.900   5.78  
29  15  C8     N9     C4     102.651  105.800  0.400  -7.87  
30  15  N1     C2     N3     126.796  129.300  0.500  -5.01  
31  15  N7     C8     N9     117.503  113.800  0.500   7.41  
32  16  C8     N9     C4     103.725  106.400  0.400  -6.69  
33  16  N7     C8     N9     117.316  113.100  0.500   8.43  
34  16  "O4'"  "C1'"  N9     112.987  108.000  0.700   7.12  
35  17  "C4'"  "C3'"  "C2'"  109.530  103.100  0.900   7.14  
36  17  C8     N9     C4     103.672  105.800  0.400  -5.32  
37  17  N7     C8     N9     117.402  113.800  0.500   7.20  
38  18  "C4'"  "C3'"  "C2'"  108.675  103.100  0.900   6.20  
39  18  "O4'"  "C1'"  N1     112.928  108.000  0.700   7.04  
40  19  "C4'"  "C3'"  "C2'"  108.850  103.100  0.900   6.39  
41  20  "C4'"  "C3'"  "C2'"  108.362  103.100  0.900   5.85  
42  20  C8     N9     C4     103.278  105.800  0.400  -6.30  
43  20  N1     C2     N3     126.729  129.300  0.500  -5.14  
44  20  N7     C8     N9     117.552  113.800  0.500   7.50  
45  20  "O4'"  "C1'"  N9     111.622  108.000  0.700   5.17  
46  21  "C4'"  "C3'"  "C2'"  108.212  103.100  0.900   5.68  
47  21  C8     N9     C4     103.729  106.400  0.400  -6.68  
48  21  N7     C8     N9     117.458  113.100  0.500   8.71  
49  22  "C4'"  "C3'"  "C2'"  107.674  103.100  0.900   5.08  
50  22  N1     C2     N3     126.796  129.300  0.500  -5.01  
51  22  N7     C8     N9     117.428  113.800  0.500   7.26  
52  23  C8     N9     C4     103.042  106.400  0.400  -8.39  
53  23  N7     C8     N9     117.488  113.100  0.500   8.78  
54  23  "O4'"  "C1'"  N9     111.693  108.000  0.700   5.28  
55  24  "C4'"  "C3'"  "C2'"  109.139  103.100  0.900   6.71  
56  24  C8     N9     C4     103.693  106.400  0.400  -6.77  
57  24  N7     C8     N9     117.599  113.100  0.500   9.00  
#
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        "1.8.5 (274361), CSD as541be (2020)"                                  Y  
3  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
