data_7JP7

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7JP7
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7JP7
_pdbx_vrpt_summary.PDB_deposition_date         2020-08-07
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-18
_pdbx_vrpt_summary.report_creation_date        2023-10-09:05:21
_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*GP*CP*AP*GP*AP*CP*GP*TP*GP*AP*CP*GP*CP*CP*AP*CP*TP*CP*A)-3')"  
2  polymer      "DNA (5'-D(P*GP*CP*GP*TP*CP*A)-3')"  
3  polymer      "DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*G)-3')"  
4  polymer      "DNA (5'-D(P*CP*GP*TP*CP*TP*GP*C)-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  
F  5  
G  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  3.207  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   23.48  141614     ?     ?  
2  2  1   58.18    1253  3.20  3.20  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1095  3.20  3.20  
5  1  3   27.11  130704     ?     ?  
6  2  3   69.48    1133  3.20  3.20  
#
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  0.90  0.62  481  740  
2  1  2  B  B  1.00  0.62  137  209  
3  1  3  C  C  1.08  0.70  182  280  
4  1  4  D  D  1.00  0.57  156  238  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       11.24
_pdbx_vrpt_summary_geometry.num_H_reduce     476
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.63
_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            64.962
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         85.299
_pdbx_vrpt_summary_diffraction.I_over_sigma              5.12(3.18A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3610
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.154
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.460
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.286
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.966
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.071;h,-h-k,-l:0.085;-k,-h,-l:0.095
_pdbx_vrpt_summary_diffraction.DCC_R                     0.24
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.25
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.21
_pdbx_vrpt_summary_diffraction.EDS_res_low               34.08
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[81.681,81.681,248.779,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           1.216
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 8.04% 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         21
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         78.65
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      184
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.10
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.21
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        34.08
_pdbx_vrpt_summary_diffraction.PDB_R                     0.24
_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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  DG   A    1  .  ?        ?     ?  
 2  1  1  A   2  DA   A    2  .  ?        ?     ?  
 3  1  1  A   3  DG   A    3  .  ?        ?     1  
 4  1  1  A   4  DC   A    4  .  ?        ?     3  
 5  1  1  A   5  DA   A    5  .  ?        ?     2  
 6  1  1  A   6  DG   A    6  .  ?        ?     ?  
 7  1  1  A   7  DA   A    7  .  ?        ?     ?  
 8  1  1  A   8  DC   A    8  .  ?        ?     ?  
 9  1  1  A   9  DG   A    9  .  ?        ?     1  
10  1  1  A  10  DT   A   10  .  ?        ?     1  
11  1  1  A  11  DG   A   11  .  ?        ?     ?  
12  1  1  A  12  DA   A   12  .  ?        ?     ?  
13  1  1  A  13  DC   A   13  .  ?        ?     ?  
14  1  1  A  14  DG   A   14  .  ?        ?     ?  
15  1  1  A  15  DC   A   15  .  ?        ?     1  
16  1  1  A  16  DC   A   16  .  ?        ?     1  
17  1  1  A  17  DA   A   17  .  ?        ?     ?  
18  1  1  A  18  DC   A   18  .  ?        ?     ?  
19  1  1  A  19  DT   A   19  .  ?        ?     1  
20  1  1  A  20  DC   A   20  .  ?        ?     1  
21  1  1  A  21  DA   A   21  .  ?        ?     ?  
22  1  2  B   1  DG   B    0  .  ?        ?     2  
23  1  2  B   2  DC   B    1  .  ?        ?     2  
24  1  2  B   3  DG   B    2  .  ?        ?     2  
25  1  2  B   4  DT   B    3  .  ?        ?     2  
26  1  2  B   5  DC   B    4  .  ?        ?     1  
27  1  2  B   6  DA   B    5  .  ?        ?     ?  
28  1  3  C   1  DT   C    1  .  ?        ?     3  
29  1  3  C   2  DC   C    2  .  ?        ?     1  
30  1  3  C   3  DT   C    3  .  ?        ?     ?  
31  1  3  C   4  DG   C    4  .  ?        ?     ?  
32  1  3  C   5  DA   C    5  .  ?        ?     1  
33  1  3  C   6  DG   C    6  .  ?        ?     1  
34  1  3  C   7  DT   C    7  .  ?        ?     ?  
35  1  3  C   8  DG   C    8  .  ?        ?     1  
36  1  4  D   1  DC   D   10  .  ?        ?     ?  
37  1  4  D   2  DG   D   11  .  ?        ?     ?  
38  1  4  D   3  DT   D   12  .  ?        1     1  
39  1  4  D   4  DC   D   13  .  ?        ?     1  
40  1  4  D   5  DT   D   14  .  ?        ?     ?  
41  1  4  D   6  DG   D   15  .  ?        ?     ?  
42  1  4  D   7  DC   D   16  .  ?        ?     ?  
43  1  5  E   .  CAC  A  101  .  ?        ?     ?  
44  1  5  F   .  CAC  A  102  .  ?        ?     ?  
45  1  5  G   .  CAC  D  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  114.690    22  0.48    35  1.00  molprobity  1.000  
 2   2    11  125.960    24  0.54    37  0.85  molprobity  1.000  
 3   3    11  134.750    25  0.62    39  0.84  molprobity  1.000  
 4   4    11  142.460    21  0.53    32  0.80  molprobity  1.000  
 5   5    11  138.730    24  0.62    37  0.81  molprobity  1.000  
 6   6    11  139.060    25  0.84    39  0.90  molprobity  1.000  
 7   7    11  145.920    24  0.95    37  0.96  molprobity  1.000  
 8   8    11  142.100    21  0.55    32  0.85  molprobity  1.000  
 9   9    11  126.290    25  0.47    39  0.98  molprobity  1.000  
10  10    12  132.910    22  0.53    34  1.35  molprobity  1.000  
11  11    11  121.380    25  0.60    39  0.81  molprobity  1.000  
12  12    11  114.420    24  0.57    37  0.66  molprobity  1.000  
13  13    11  112.140    21  0.69    32  1.11  molprobity  1.000  
14  14    11  120.630    25  0.63    39  0.88  molprobity  1.000  
15  15    11  121.350    21  0.54    32  0.83  molprobity  1.000  
16  16    11  119.880    21  0.58    32  0.70  molprobity  1.000  
17  17    11  118.810    24  0.52    37  0.55  molprobity  1.000  
18  18    11  108.270    21  0.37    32  0.81  molprobity  1.000  
19  19    12  106.040    22  0.78    34  1.33  molprobity  1.000  
20  20    11  114.780    21  0.61    32  0.75  molprobity  1.000  
21  21    12  117.860    23  0.56    33  0.73  molprobity  1.000  
22  22    11   99.300    25  0.43    39  0.93  molprobity  1.000  
23  23    11   93.560    21  0.54    32  0.83  molprobity  1.000  
24  24    11  106.850    25  0.81    39  0.86  molprobity  1.000  
25  25    12  115.140    22  0.68    34  1.50  molprobity  1.000  
26  26    11   97.730    21  0.49    32  1.09  molprobity  1.000  
27  27    12   90.400    23  0.65    33  0.55  molprobity  1.000  
28  28    13  114.190    19  0.49    30  1.45  molprobity  1.000  
29  29    11  125.900    21  0.55    32  0.79  molprobity  1.000  
30  30    12  133.360    22  1.15    34  1.41  molprobity  1.000  
31  31    11  131.820    25  0.73    39  0.67  molprobity  1.000  
32  32    11  127.900    24  0.59    37  0.82  molprobity  1.000  
33  33    11  111.720    25  0.61    39  1.03  molprobity  1.000  
34  34    12   92.520    22  0.78    34  1.52  molprobity  1.000  
35  35    12   86.560    24  0.48    35  0.63  molprobity  1.000  
36  36    11   96.570    21  0.47    32  0.66  molprobity  1.000  
37  37    11  111.960    25  0.51    39  0.74  molprobity  1.000  
38  38    12  126.100    22  0.66    34  1.50  molprobity  1.000  
39  39    11  144.120    21  0.67    32  1.02  molprobity  1.000  
40  40    12  161.320    22  0.63    34  1.30  molprobity  1.000  
41  41    11  157.740    25  0.58    39  0.80  molprobity  1.000  
42  42    12  150.700    20  0.44    28  0.66  molprobity  1.000  
43  43     ?  174.390     ?     ?     ?     ?  ?           1.000  
44  44     ?  184.190     ?     ?     ?     ?  ?           1.000  
45  45     ?  171.350     ?     ?     ?     ?  ?           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   3  "H2'"    1  0.40  2.57  
 2   4  "H2'"    2  0.46  2.51  
 3   4  "H2''"   3  0.40  2.21  
 4   4  C6       1  0.40  2.57  
 5   5  C8       2  0.46  2.51  
 6   5  "O4'"    3  0.40  2.21  
 7   9  "H2'"    4  0.50  1.93  
 8  10  H71      4  0.50  1.93  
 9  15  C2       5  0.52  2.98  
10  16  C5       5  0.52  2.98  
11  19  "H2''"   6  0.42  2.55  
12  20  C6       6  0.42  2.55  
13  22  "O4'"    7  0.47  2.14  
14  22  "H2'"    8  0.45  2.52  
15  23  C6       8  0.45  2.52  
16  23  "H2'"    9  0.44  2.53  
17  24  "H2'"   10  0.51  1.92  
18  24  C8       9  0.44  2.53  
19  25  H71     10  0.51  1.92  
20  25  "H2''"  11  0.40  2.03  
21  26  "H5'"   11  0.40  2.03  
22  28  H6      12  0.43  1.65  
23  28  "HO5'"  12  0.43  1.65  
24  28  "H2''"  13  0.41  2.56  
25  29  C6      13  0.41  2.56  
26  32  "H2''"  14  0.45  1.97  
27  33  "H5''"  14  0.45  1.97  
28  35  "H2''"   7  0.47  2.14  
29  38  "H2''"  15  0.42  2.49  
30  39  "C5'"   15  0.42  2.49  
#
_pdbx_vrpt_instance_intra_angle_outliers.ordinal      1
_pdbx_vrpt_instance_intra_angle_outliers.instance_id  38
_pdbx_vrpt_instance_intra_angle_outliers.atom_1       N3
_pdbx_vrpt_instance_intra_angle_outliers.atom_2       C4
_pdbx_vrpt_instance_intra_angle_outliers.atom_3       O4
_pdbx_vrpt_instance_intra_angle_outliers.obs          122.927
_pdbx_vrpt_instance_intra_angle_outliers.mean         119.900
_pdbx_vrpt_instance_intra_angle_outliers.stdev        0.600
_pdbx_vrpt_instance_intra_angle_outliers.Z            5.04
#
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  0.914  0.118  -0.943  
 2   2  21  0.946  0.069  -1.578  
 3   3  22  0.912  0.092  -1.265  
 4   4  19  0.927  0.080  -1.421  
 5   5  21  0.925  0.122  -0.911  
 6   6  22  0.962  0.053  -1.748  
 7   7  21  0.954  0.069  -1.578  
 8   8  19  0.964  0.069  -1.548  
 9   9  22  0.928  0.077  -1.451  
10  10  20  0.913  0.095  -1.293  
11  11  22  0.968  0.071  -1.525  
12  12  21  0.940  0.090  -1.314  
13  13  19  0.933  0.091  -1.293  
14  14  22  0.929  0.077  -1.451  
15  15  19  0.901  0.084  -1.374  
16  16  19  0.942  0.070  -1.537  
17  17  21  0.949  0.070  -1.565  
18  18  19  0.903  0.121  -0.946  
19  19  20  0.921  0.135  -0.835  
20  20  19  0.947  0.113  -1.038  
21  21  21  0.923  0.115  -0.999  
22  22  22  0.910  0.101  -1.154  
23  23  19  0.942  0.094  -1.258  
24  24  22  0.944  0.083  -1.377  
25  25  20  0.896  0.111  -1.110  
26  26  19  0.947  0.106  -1.119  
27  27  21  0.926  0.146  -0.608  
28  28  17  0.961  0.077  -1.499  
29  29  19  0.915  0.096  -1.235  
30  30  20  0.904  0.102  -1.213  
31  31  22  0.920  0.082  -1.389  
32  32  21  0.962  0.080  -1.440  
33  33  22  0.927  0.087  -1.327  
34  34  20  0.915  0.129  -0.904  
35  35  22  0.856  0.168  -0.323  
36  36  19  0.930  0.125  -0.899  
37  37  22  0.938  0.076  -1.463  
38  38  20  0.904  0.104  -1.190  
39  39  19  0.917  0.088  -1.328  
40  40  20  0.915  0.066  -1.625  
41  41  22  0.946  0.068  -1.563  
42  42  19  0.931  0.120  -0.957  
43  43   1  0.878  0.188       ?  
44  44   1  0.850  0.115       ?  
45  45   1  0.900  0.141       ?  
#
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  
##
