data_7TGB

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7TGB
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7TGB
_pdbx_vrpt_summary.PDB_deposition_date         2022-01-07
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2023-02-01
_pdbx_vrpt_summary.report_creation_date        2023-01-25:23:02
_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"  
#
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  5.36  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   1.62  141614     ?     ?  
2  2  1  14.33    1012  3.86  6.86  
3  1  2  84.49  130704     ?     ?  
4  2  2  99.74    1186  3.80  6.92  
#
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  1.44  1.37  481  741  
2  1  2  B  B  1.46  1.53  156  237  
3  1  3  C  C  1.22  1.00  160  245  
4  1  4  D  D  1.27  1.31  161  245  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       43.38
_pdbx_vrpt_summary_geometry.num_H_reduce     477
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   958
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.33
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1468
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.38
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            999.000
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         271.247
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.60(5.40A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1078
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.133
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.486
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.325
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.869
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.051
_pdbx_vrpt_summary_diffraction.DCC_R                     0.16
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.20
_pdbx_vrpt_summary_diffraction.EDS_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_res_high              5.36
_pdbx_vrpt_summary_diffraction.EDS_res_low               64.86
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[268.711,268.711,454.484,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.562
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 8.64% 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         69.19
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      39
_pdbx_vrpt_summary_diffraction.percent_free_reflections  3.62
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       5.36
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        41.02
_pdbx_vrpt_summary_diffraction.PDB_R                     0.15
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.19
#
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_symm_clashes
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A   1  DG  A    1  .  ?        ?     ?     4     1  ?     
 2  1  1  A   2  DA  A    2  .  ?        ?     ?     7     ?  ?     
 3  1  1  A   3  DG  A    3  .  ?        ?     1     4     ?  ?     
 4  1  1  A   4  DC  A    4  .  ?        1     ?     5     ?  ?     
 5  1  1  A   5  DA  A    5  .  ?        ?     ?     2     ?  ?     
 6  1  1  A   6  DG  A    6  .  ?        ?     ?     2     ?  ?     
 7  1  1  A   7  DC  A    7  .  ?        ?     1     3     ?  ?     
 8  1  1  A   8  DC  A    8  .  ?        ?     ?     6     ?  ?     
 9  1  1  A   9  DT  A    9  .  ?        ?     1     2     ?  ?     
10  1  1  A  10  DG  A   10  .  ?        1     ?     5     ?  ?     
11  1  1  A  11  DT  A   11  .  ?        ?     3     8     ?  ?     
12  1  1  A  12  DT  A   12  .  ?        ?     ?     7     ?  ?     
13  1  1  A  13  DT  A   13  .  ?        2     2     4     ?  ?     
14  1  1  A  14  DG  A   14  .  ?        ?     ?     2     ?  ?     
15  1  1  A  15  DG  A   15  .  ?        ?     ?     4     ?  ?     
16  1  1  A  16  DA  A   16  .  ?        ?     ?     4     ?  ?     
17  1  1  A  17  DC  A   17  .  ?        ?     ?     1     ?  ?     
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  .  ?        ?     ?     3     ?  ?     
21  1  1  A  21  DA  A   21  .  ?        ?     ?     2     ?  ?     
22  1  2  B   1  DC  B    1  .  ?        ?     ?     ?     ?  ?     
23  1  2  B   2  DC  B    2  .  ?        ?     ?     2     ?  ?     
24  1  2  B   3  DA  B    3  .  ?        1     ?     2     ?  ?     
25  1  2  B   4  DT  B    4  .  ?        ?     2     2     ?  ?     
26  1  2  B   5  DA  B    5  .  ?        ?     ?     2     ?  ?     
27  1  2  B   6  DC  B    6  .  ?        ?     ?     ?     ?  ?     
28  1  2  B   7  DA  B    7  .  ?        ?     1     2     ?  ?     
29  1  3  C   1  DG  C    8  .  ?        ?     ?     5     ?  ?     
30  1  3  C   2  DG  C    9  .  ?        ?     ?     1     ?  ?     
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  .  ?        ?     2     ?     ?  ?     
36  1  4  D   1  DC  D    1  .  ?        1     ?     1     1  ?     
37  1  4  D   2  DT  D    2  .  ?        ?     ?     6     ?  ?     
38  1  4  D   3  DG  D    3  .  ?        ?     ?     5     ?  ?     
39  1  4  D   4  DA  D    4  .  ?        ?     ?     2     ?  ?     
40  1  4  D   5  DT  D    5  .  ?        ?     1     2     ?  ?     
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     
44  1  5  F   .  HG  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.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  1.24  35  1.31  molprobity  
 2   2  11  24  1.13  37  1.38  molprobity  
 3   3  11  25  0.90  39  1.52  molprobity  
 4   4  11  21  1.89  32  1.47  molprobity  
 5   5  11  24  0.92  37  0.82  molprobity  
 6   6  11  25  0.89  39  0.85  molprobity  
 7   7  11  21  1.42  32  1.81  molprobity  
 8   8  11  21  1.58  32  1.49  molprobity  
 9   9  12  22  1.13  34  1.80  molprobity  
10  10  11  25  1.81  39  1.64  molprobity  
11  11  12  22  1.86  34  2.13  molprobity  
12  12  12  22  1.95  34  1.88  molprobity  
13  13  12  22  2.42  34  2.01  molprobity  
14  14  11  25  1.21  39  1.19  molprobity  
15  15  11  25  1.34  39  1.49  molprobity  
16  16  11  24  1.01  37  0.88  molprobity  
17  17  11  21  0.78  32  0.95  molprobity  
18  18  11  24  1.09  37  1.05  molprobity  
19  19  12  22  1.22  34  1.51  molprobity  
20  20  11  21  0.94  32  1.25  molprobity  
21  21  12  23  0.78  33  0.89  molprobity  
22  22  11  21  1.04  32  1.13  molprobity  
23  23  11  21  1.50  32  1.01  molprobity  
24  24  11  24  1.97  37  1.39  molprobity  
25  25  11  22  1.77  34  2.02  molprobity  
26  26  11  24  1.62  37  1.41  molprobity  
27  27  11  21  1.01  32  1.36  molprobity  
28  28  12  23  1.42  33  1.63  molprobity  
29  29  11  25  0.87  39  1.22  molprobity  
30  30  11  25  1.06  39  1.15  molprobity  
31  31  11  21  1.36  32  1.00  molprobity  
32  32  12  22  0.89  34  1.57  molprobity  
33  33  11  25  0.85  39  0.85  molprobity  
34  34  11  21  0.87  32  0.91  molprobity  
35  35  13  21  1.04  30  1.66  molprobity  
36  36  11  22  2.40  32  1.21  molprobity  
37  37  12  22  0.97  34  1.45  molprobity  
38  38  11  25  1.09  39  1.41  molprobity  
39  39  11  24  1.17  37  0.74  molprobity  
40  40  12  22  0.85  34  1.46  molprobity  
41  41  11  25  0.97  39  1.04  molprobity  
42  42  13  21  1.12  30  1.47  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  "H3'"    1  0.62  1.64  
  2   1  "H3'"    2  0.49  2.46  
  3   1  "H2'"    3  0.47  2.29  
  4   1  N3       3  0.47  2.29  
  5   2  H8       1  0.62  1.64  
  6   2  H8       4  0.44  2.00  
  7   2  C8       2  0.49  2.46  
  8   2  "H2'"    5  0.47  2.13  
  9   2  OP2      5  0.47  2.13  
 10   2  OP2      4  0.44  2.00  
 11   2  "H1'"    6  0.47  2.14  
 12   3  "H2''"   7  0.65  1.97  
 13   3  OP2      6  0.47  2.14  
 14   3  C4       8  0.46  3.04  
 15   3  C2       9  0.41  3.08  
 16   4  "O5'"    7  0.65  1.97  
 17   4  "H2'"   10  0.56  2.41  
 18   4  C6       8  0.46  3.04  
 19   4  C2       9  0.41  3.08  
 20   4  "H2''"  11  0.40  2.20  
 21   5  C8      10  0.56  2.41  
 22   5  OP1     11  0.40  2.20  
 23   6  C6      12  0.47  3.03  
 24   6  C5      13  0.46  3.03  
 25   7  C4      12  0.47  3.03  
 26   7  C5      13  0.46  3.03  
 27   7  "H2''"  14  0.40  2.56  
 28   8  "H5''"  15  0.64  1.62  
 29   8  "H5''"  16  0.52  2.44  
 30   8  H6      15  0.64  1.62  
 31   8  "H2'"   17  0.53  2.43  
 32   8  C6      16  0.52  2.44  
 33   8  C5      14  0.40  2.56  
 34   9  "H2'"   18  0.60  2.35  
 35   9  C6      17  0.53  2.43  
 36  10  C8      18  0.60  2.35  
 37  10  "H5''"  19  0.58  1.84  
 38  10  "H5''"  20  0.42  2.50  
 39  10  "H2'"   21  0.51  2.45  
 40  10  "H2'"   22  0.47  2.50  
 41  11  "H2''"  23  0.59  2.01  
 42  11  "H2''"  24  0.45  1.99  
 43  11  H72     19  0.58  1.84  
 44  11  C5      21  0.51  2.45  
 45  11  C6      22  0.47  2.50  
 46  11  "H1'"   25  0.46  2.15  
 47  11  "H1'"   26  0.43  2.58  
 48  11  C7      20  0.42  2.50  
 49  12  "H1'"   27  0.61  1.82  
 50  12  "H1'"   28  0.53  2.38  
 51  12  OP1     23  0.59  2.01  
 52  12  OP2     25  0.46  2.15  
 53  12  H71     24  0.45  1.99  
 54  12  P       26  0.43  2.58  
 55  12  "H2''"  29  0.41  2.20  
 56  13  "H5'"   27  0.61  1.82  
 57  13  "C5'"   28  0.53  2.38  
 58  13  "H2''"  30  0.52  2.25  
 59  13  "O5'"   29  0.41  2.20  
 60  14  "H2''"  31  0.53  2.42  
 61  14  N7      30  0.52  2.25  
 62  15  "H2''"  32  0.65  1.95  
 63  15  C8      31  0.53  2.42  
 64  15  "H2'"   33  0.43  2.53  
 65  15  "C2'"   34  0.40  3.05  
 66  16  "H1'"   35  0.75  1.68  
 67  16  "O5'"   32  0.65  1.95  
 68  16  C8      33  0.43  2.53  
 69  16  C8      34  0.40  3.05  
 70  17  "H5'"   35  0.75  1.68  
 71  19  "H2''"  36  0.42  2.20  
 72  20  "H2''"  37  0.44  2.53  
 73  20  "C2'"   38  0.42  3.03  
 74  20  "O5'"   36  0.42  2.20  
 75  21  C8      37  0.44  2.53  
 76  21  C8      38  0.42  3.03  
 77  23  "H2''"  39  0.64  2.12  
 78  23  "H2''"  40  0.53  2.43  
 79  24  N7      39  0.64  2.12  
 80  24  C5      40  0.53  2.43  
 81  25  "H1'"   41  0.58  1.86  
 82  25  C4      42  0.42  3.08  
 83  26  "H5'"   41  0.58  1.86  
 84  26  C6      42  0.42  3.08  
 85  28  N1      43  0.49  2.81  
 86  28  C6      44  0.48  3.01  
 87  29  "H2'"   45  0.52  2.24  
 88  29  N3      45  0.52  2.24  
 89  29  C2      43  0.49  2.81  
 90  29  C2      44  0.48  3.01  
 91  29  "H3'"   46  0.45  2.52  
 92  30  C8      46  0.45  2.52  
 93  32  "H2'"   47  0.66  2.30  
 94  32  "H2''"  48  0.51  2.09  
 95  33  C8      47  0.66  2.30  
 96  33  OP1     48  0.51  2.09  
 97  36  "H1'"   49  0.42  2.20  
 98  37  "H2'"   50  0.81  2.15  
 99  37  "H2'"   51  0.65  1.59  
100  37  "H2''"  52  0.51  2.10  
101  37  "H2''"  53  0.46  2.45  
102  37  N3      54  0.43  2.87  
103  37  OP2     49  0.42  2.20  
104  38  C8      50  0.81  2.15  
105  38  H8      51  0.65  1.59  
106  38  "O5'"   52  0.51  2.10  
107  38  "C5'"   53  0.46  2.45  
108  38  C5      54  0.43  2.87  
109  39  "H2''"  55  0.73  1.71  
110  39  "H2''"  56  0.40  2.48  
111  40  H71     55  0.73  1.71  
112  40  C7      56  0.40  2.48  
113  41  "H2''"  57  0.72  1.71  
114  42  "H5''"  57  0.72  1.71  
#
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  O6  0  1_555  0.09  2.11  
2  36  N4  0  4_445  0.09  2.11  
#
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   4  "C1'"  N1     1.564  1.488  0.013    5.83  
2  10  "C3'"  "O3'"  1.365  1.435  0.013   -5.41  
3  13  "C1'"  N1     1.375  1.468  0.014   -6.63  
4  13  "C3'"  "O3'"  1.359  1.435  0.013   -5.88  
5  24  N9     C4     1.340  1.374  0.006   -5.68  
6  36  OP3    P      1.479  1.607  0.012  -10.70  
#
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   3  "O5'"  P      OP2  100.686  105.700  0.900  -5.57  
 2   7  "O4'"  "C1'"  N1   111.548  108.000  0.700   5.07  
 3   9  N3     C4     O4   123.272  119.900  0.600   5.62  
 4  11  C5     C4     O4   121.335  124.900  0.700  -5.09  
 5  11  N3     C4     O4   123.067  119.900  0.600   5.28  
 6  11  "O4'"  "C1'"  N1   112.712  108.000  0.700   6.73  
 7  13  C5     C4     O4   120.760  124.900  0.700  -5.91  
 8  13  N3     C4     O4   124.009  119.900  0.600   6.85  
 9  25  C5     C4     O4   120.905  124.900  0.700  -5.71  
10  25  N3     C4     O4   123.002  119.900  0.600   5.17  
11  28  "O4'"  "C1'"  N9   112.132  108.000  0.700   5.90  
12  35  C5     C4     O4   121.069  124.900  0.700  -5.47  
13  35  N3     C4     O4   123.587  119.900  0.600   6.14  
14  40  N3     C4     O4   123.050  119.900  0.600   5.25  
#
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          2.31.2                                                                Y  
4  dcc          "2.26  (2020-01-20)"                                                  Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
