data_7JI6

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7JI6
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7JI6
_pdbx_vrpt_summary.PDB_deposition_date         2020-07-22
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-18
_pdbx_vrpt_summary.report_creation_date        2023-10-10:22:23
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*AP*AP*GP*A)-3')"  
2  polymer      "DNA (5'-D(P*CP*GP*TP*CP*GP*AP*CP*TP*C)-3')"  
3  polymer      "DNA (5'-D(P*TP*CP*TP*AP*CP*G)-3')"  
4  polymer      "DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*GP*TP*TP*GP*TP*CP*GP*T)-3')"  
5  non-polymer  "CACODYLATE 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  3.005  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   21.29  141614     ?     ?  
2  2  1   57.45    2416  3.00  3.00  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1990  3.00  3.00  
5  1  3   46.99  130704     ?     ?  
6  2  3   84.74    2092  3.00  3.00  
#
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  0.79  0.64  281  432  
2  1  2  B  B  0.91  0.69  201  307  
3  1  3  C  C  1.17  0.86  134  204  
4  1  4  D  D  1.03  0.69  340  524  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       11.99
_pdbx_vrpt_summary_geometry.num_H_reduce     478
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.70
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1467
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.97
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            28.574
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         92.482
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.40(3.01A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        4470
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.123
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.466
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.296
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.974
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.065
_pdbx_vrpt_summary_diffraction.DCC_R                     0.21
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.23
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.01
_pdbx_vrpt_summary_diffraction.EDS_res_low               45.33
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[79.687,79.687,153.898,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.711
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 6.32% 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         93.81
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      218
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.88
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        45.33
_pdbx_vrpt_summary_diffraction.PDB_R                     0.21
_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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  DG   A    1  .  ?        ?     1  
 2  1  1  A   2  DA   A    2  .  ?        ?     1  
 3  1  1  A   3  DA   A    3  .  ?        ?     ?  
 4  1  1  A   4  DC   A    4  .  ?        ?     ?  
 5  1  1  A   5  DG   A    5  .  ?        ?     ?  
 6  1  1  A   6  DA   A    6  .  ?        ?     ?  
 7  1  1  A   7  DC   A    7  .  ?        ?     ?  
 8  1  1  A   8  DA   A    8  .  ?        ?     1  
 9  1  1  A   9  DA   A    9  .  ?        ?     1  
10  1  1  A  10  DA   A   10  .  ?        ?     1  
11  1  1  A  11  DG   A   11  .  ?        ?     ?  
12  1  1  A  12  DA   A   12  .  ?        ?     ?  
13  1  2  B   1  DC   B   12  .  ?        ?     ?  
14  1  2  B   2  DG   B   13  .  ?        ?     ?  
15  1  2  B   3  DT   B   14  .  ?        ?     ?  
16  1  2  B   4  DC   B   15  .  ?        ?     1  
17  1  2  B   5  DG   B   16  .  ?        ?     1  
18  1  2  B   6  DA   B   17  .  ?        ?     ?  
19  1  2  B   7  DC   B   18  .  ?        ?     ?  
20  1  2  B   8  DT   B   19  .  ?        ?     ?  
21  1  2  B   9  DC   B   20  .  ?        ?     ?  
22  1  3  C   1  DT   C    0  .  ?        ?     ?  
23  1  3  C   2  DC   C    1  .  ?        ?     ?  
24  1  3  C   3  DT   C    2  .  ?        1     ?  
25  1  3  C   4  DA   C    3  .  ?        ?     1  
26  1  3  C   5  DC   C    4  .  ?        ?     2  
27  1  3  C   6  DG   C    5  .  ?        ?     1  
28  1  4  D   1  DT   D    2  .  ?        ?     ?  
29  1  4  D   2  DC   D    3  .  ?        ?     2  
30  1  4  D   3  DG   D    4  .  ?        ?     ?  
31  1  4  D   4  DA   D    5  .  ?        ?     1  
32  1  4  D   5  DG   D    6  .  ?        ?     1  
33  1  4  D   6  DT   D    7  .  ?        ?     ?  
34  1  4  D   7  DC   D    8  .  ?        ?     ?  
35  1  4  D   8  DG   D    9  .  ?        ?     ?  
36  1  4  D   9  DT   D   10  .  ?        ?     1  
37  1  4  D  10  DT   D   11  .  ?        ?     1  
38  1  4  D  11  DG   D   12  .  ?        ?     2  
39  1  4  D  12  DT   D   13  .  ?        ?     1  
40  1  4  D  13  DC   D   14  .  ?        ?     1  
41  1  4  D  14  DG   D   15  .  ?        ?     2  
42  1  4  D  15  DT   D   16  .  ?        ?     1  
43  1  5  E   .  CAC  C  101  .  ?        ?     ?  
#
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  108.530    22  0.75    35  0.72  molprobity  1.000  
 2   2    11  118.500    24  0.81    37  0.71  molprobity  1.000  
 3   3    11  114.660    24  0.45    37  0.69  molprobity  1.000  
 4   4    11  107.110    21  0.61    32  0.84  molprobity  1.000  
 5   5    11  102.960    25  0.53    39  0.66  molprobity  1.000  
 6   6    11  100.000    24  0.47    37  0.84  molprobity  1.000  
 7   7    11   99.340    21  0.74    32  0.91  molprobity  1.000  
 8   8    11   97.610    24  0.59    37  0.69  molprobity  1.000  
 9   9    11   99.290    24  0.66    37  0.72  molprobity  1.000  
10  10    11  102.230    24  0.80    37  0.66  molprobity  1.000  
11  11    11   94.400    25  0.57    39  0.75  molprobity  1.000  
12  12    12   82.420    23  0.65    33  1.25  molprobity  1.000  
13  13    11   79.410    21  0.81    32  0.83  molprobity  1.000  
14  14    11   78.370    25  0.72    39  0.80  molprobity  1.000  
15  15    12   84.760    22  0.74    34  1.33  molprobity  1.000  
16  16    11   82.250    21  0.58    32  0.80  molprobity  1.000  
17  17    11   87.180    25  0.53    39  0.58  molprobity  1.000  
18  18    11   86.020    24  0.70    37  0.68  molprobity  1.000  
19  19    11   87.060    21  0.99    32  0.99  molprobity  1.000  
20  20    12   93.990    22  0.45    34  1.20  molprobity  1.000  
21  21    12  103.420    20  0.51    28  0.75  molprobity  1.000  
22  22    12   86.540    22  0.38    34  1.23  molprobity  1.000  
23  23    11   81.000    21  1.03    32  1.27  molprobity  1.000  
24  24    12   72.070    22  0.83    34  1.69  molprobity  1.000  
25  25    11   67.590    24  1.25    37  1.06  molprobity  1.000  
26  26    11   70.230    21  0.82    32  0.78  molprobity  1.000  
27  27    12   81.410    24  0.58    35  0.75  molprobity  1.000  
28  28    13  115.330    19  0.78    30  1.41  molprobity  1.000  
29  29    11  117.110    21  0.77    32  0.92  molprobity  1.000  
30  30    11  108.120    25  0.64    39  0.70  molprobity  1.000  
31  31    11   99.490    24  0.61    37  0.76  molprobity  1.000  
32  32    11   84.260    25  0.81    39  0.91  molprobity  1.000  
33  33    12   74.820    22  0.80    34  1.41  molprobity  1.000  
34  34    11   65.740    21  0.70    32  0.77  molprobity  1.000  
35  35    11   62.160    25  0.88    39  0.89  molprobity  1.000  
36  36    12   75.080    22  0.81    34  1.28  molprobity  1.000  
37  37    12   80.530    22  0.60    34  1.22  molprobity  1.000  
38  38    11   91.020    25  0.67    39  0.90  molprobity  1.000  
39  39    12  104.380    22  0.36    34  1.24  molprobity  1.000  
40  40    11  113.810    21  0.56    32  0.78  molprobity  1.000  
41  41    11  120.600    25  0.59    39  0.81  molprobity  1.000  
42  42    13  122.130    21  0.57    30  1.25  molprobity  1.000  
43  43     ?  120.320     ?     ?     ?     ?  ?           1.000  
#
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  0.60  2.37  
 2   2  C8       1  0.60  2.37  
 3   8  C2       2  0.40  3.09  
 4   9  C2       3  0.45  3.05  
 5  10  C5       3  0.45  3.05  
 6  16  "H2''"   4  0.58  2.39  
 7  17  C8       4  0.58  2.39  
 8  25  "H2'"    5  0.42  2.55  
 9  26  "H2''"   6  0.43  2.18  
10  26  C6       5  0.42  2.55  
11  27  "O5'"    6  0.43  2.18  
12  29  "H5''"   7  0.44  1.82  
13  29  H6       7  0.44  1.82  
14  31  "H2''"   8  0.44  1.99  
15  32  "H5''"   8  0.44  1.99  
16  36  "H2'"    9  0.59  2.38  
17  37  C6       9  0.59  2.38  
18  38  "H2''"  10  0.54  1.90  
19  38  C2       2  0.40  3.09  
20  39  "H5''"  10  0.54  1.90  
21  40  "H2'"   11  0.51  2.45  
22  41  C8      11  0.51  2.45  
23  41  "H2''"  12  0.43  2.18  
24  42  "O5'"   12  0.43  2.18  
#
_pdbx_vrpt_instance_intra_angle_outliers.ordinal      1
_pdbx_vrpt_instance_intra_angle_outliers.instance_id  24
_pdbx_vrpt_instance_intra_angle_outliers.atom_1       "O4'"
_pdbx_vrpt_instance_intra_angle_outliers.atom_2       "C4'"
_pdbx_vrpt_instance_intra_angle_outliers.atom_3       "C3'"
_pdbx_vrpt_instance_intra_angle_outliers.obs          102.271
_pdbx_vrpt_instance_intra_angle_outliers.mean         104.500
_pdbx_vrpt_instance_intra_angle_outliers.stdev        0.400
_pdbx_vrpt_instance_intra_angle_outliers.Z            -5.57
#
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  0.918  0.073  -1.501  
 2   2  21  0.879  0.087  -1.351  
 3   3  21  0.937  0.074  -1.515  
 4   4  19  0.932  0.088  -1.328  
 5   5  22  0.932  0.090  -1.290  
 6   6  21  0.936  0.079  -1.452  
 7   7  19  0.933  0.103  -1.154  
 8   8  21  0.925  0.095  -1.251  
 9   9  21  0.915  0.098  -1.213  
10  10  21  0.948  0.102  -1.162  
11  11  22  0.950  0.083  -1.377  
12  12  21  0.960  0.089  -1.326  
13  13  19  0.951  0.128  -0.864  
14  14  22  0.952  0.101  -1.154  
15  15  20  0.937  0.123  -0.973  
16  16  19  0.945  0.075  -1.479  
17  17  22  0.943  0.070  -1.538  
18  18  21  0.965  0.078  -1.465  
19  19  19  0.955  0.094  -1.258  
20  20  20  0.957  0.079  -1.476  
21  21  19  0.944  0.080  -1.421  
22  22  20  0.934  0.105  -1.178  
23  23  19  0.964  0.092  -1.282  
24  24  20  0.955  0.142  -0.755  
25  25  21  0.957  0.104  -1.137  
26  26  19  0.961  0.089  -1.316  
27  27  22  0.960  0.084  -1.364  
28  28  17  0.914  0.209   0.011  
29  29  19  0.899  0.153  -0.575  
30  30  22  0.898  0.093  -1.253  
31  31  21  0.908  0.103  -1.150  
32  32  22  0.927  0.095  -1.228  
33  33  20  0.955  0.102  -1.213  
34  34  19  0.963  0.108  -1.096  
35  35  22  0.958  0.115  -0.980  
36  36  20  0.954  0.098  -1.259  
37  37  20  0.924  0.110  -1.121  
38  38  22  0.947  0.094  -1.240  
39  39  20  0.913  0.100  -1.236  
40  40  19  0.904  0.095  -1.247  
41  41  22  0.911  0.132  -0.770  
42  42  20  0.931  0.178  -0.343  
43  43   1  0.980  0.105       ?  
#
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          2.35.1                                                                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  
##
