data_7JJ6

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7JJ6
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7JJ6
_pdbx_vrpt_summary.PDB_deposition_date         2020-07-24
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-18
_pdbx_vrpt_summary.report_creation_date        2023-10-09:03:53
_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*CP*AP*GP*A)-3')"  
2  polymer      "DNA (5'-D(P*CP*GP*AP*CP*GP*AP*CP*TP*C)-3')"  
3  polymer      "DNA (5'-D(P*TP*CP*TP*TP*CP*G)-3')"  
4  polymer      "DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*GP*GP*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  
F  5  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  3.077  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   19.58  141614     ?     ?  
2  2  1   49.16    1546  3.06  3.10  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1416  3.06  3.10  
5  1  3   46.99  130704     ?     ?  
6  2  3   84.95    1447  3.06  3.10  
#
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  0.81  0.66  278  427  
2  1  2  B  B  0.89  0.78  203  310  
3  1  3  C  C  1.24  0.85  132  201  
4  1  4  D  D  1.05  0.75  343  529  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       12.74
_pdbx_vrpt_summary_geometry.num_H_reduce     477
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.75
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1467
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.98
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            -10.000
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         74.565
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.89(3.06A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        4062
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.068
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.470
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.294
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.973
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.067
_pdbx_vrpt_summary_diffraction.DCC_R                     0.20
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.22
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.08
_pdbx_vrpt_summary_diffraction.EDS_res_low               35.26
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[65.106,65.106,146.300,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.881
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 5.83% 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         3
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         90.07
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      205
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.05
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.08
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        35.26
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
_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  .  ?        ?     ?  
 2  1  1  A   2  DA   A    2  .  ?        ?     2  
 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  .  ?        ?     ?  
 9  1  1  A   9  DC   A    9  .  ?        ?     ?  
10  1  1  A  10  DA   A   10  .  ?        ?     ?  
11  1  1  A  11  DG   A   11  .  ?        ?     ?  
12  1  1  A  12  DA   A   12  .  ?        ?     ?  
13  1  2  B   1  DC   B   12  .  ?        ?     1  
14  1  2  B   2  DG   B   13  .  ?        ?     1  
15  1  2  B   3  DA   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  .  ?        ?     1  
20  1  2  B   8  DT   B   19  .  ?        ?     1  
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     1  
25  1  3  C   4  DT   C    3  .  ?        ?     3  
26  1  3  C   5  DC   C    4  .  ?        ?     2  
27  1  3  C   6  DG   C    5  .  ?        ?     3  
28  1  4  D   1  DT   D    2  .  ?        ?     ?  
29  1  4  D   2  DC   D    3  .  ?        1     2  
30  1  4  D   3  DG   D    4  .  ?        ?     ?  
31  1  4  D   4  DA   D    5  .  ?        ?     ?  
32  1  4  D   5  DG   D    6  .  ?        ?     ?  
33  1  4  D   6  DT   D    7  .  ?        ?     ?  
34  1  4  D   7  DC   D    8  .  ?        ?     ?  
35  1  4  D   8  DG   D    9  .  ?        ?     1  
36  1  4  D   9  DG   D   10  .  ?        ?     1  
37  1  4  D  10  DT   D   11  .  ?        ?     1  
38  1  4  D  11  DG   D   12  .  ?        ?     ?  
39  1  4  D  12  DT   D   13  .  ?        ?     ?  
40  1  4  D  13  DC   D   14  .  ?        ?     1  
41  1  4  D  14  DG   D   15  .  ?        ?     3  
42  1  4  D  15  DT   D   16  .  ?        ?     2  
43  1  5  E   .  CAC  C  101  .  ?        ?     ?  
44  1  5  F   .  CAC  C  102  .  ?        ?     ?  
#
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   96.210    22  0.72    35  0.72  molprobity  1.000  
 2   2    11  106.710    24  0.55    37  0.63  molprobity  1.000  
 3   3    11  104.090    24  0.60    37  0.75  molprobity  1.000  
 4   4    11   99.640    21  0.58    32  0.75  molprobity  1.000  
 5   5    11   93.260    25  0.62    39  0.72  molprobity  1.000  
 6   6    11   92.170    24  0.61    37  0.69  molprobity  1.000  
 7   7    11   92.120    21  0.71    32  0.98  molprobity  1.000  
 8   8    11   86.300    24  0.56    37  0.64  molprobity  1.000  
 9   9    11   83.250    21  0.61    32  0.91  molprobity  1.000  
10  10    11   80.090    24  0.89    37  0.70  molprobity  1.000  
11  11    11   75.720    25  0.62    39  0.98  molprobity  1.000  
12  12    12   68.830    23  0.76    33  1.14  molprobity  1.000  
13  13    11   68.340    21  0.81    32  1.01  molprobity  1.000  
14  14    11   74.870    25  0.83    39  0.88  molprobity  1.000  
15  15    11   74.900    24  0.91    37  0.85  molprobity  1.000  
16  16    11   75.300    21  0.68    32  0.74  molprobity  1.000  
17  17    11   75.180    25  0.79    39  0.64  molprobity  1.000  
18  18    11   79.030    24  0.70    37  0.72  molprobity  1.000  
19  19    11   79.840    21  1.10    32  1.00  molprobity  1.000  
20  20    12   84.460    22  0.51    34  1.22  molprobity  1.000  
21  21    12   95.230    20  0.49    28  0.82  molprobity  1.000  
22  22    12   68.860    22  0.71    34  1.36  molprobity  1.000  
23  23    11   65.120    21  0.81    32  0.90  molprobity  1.000  
24  24    12   52.540    22  1.08    34  1.82  molprobity  1.000  
25  25    12   62.410    22  0.99    34  1.24  molprobity  1.000  
26  26    11   65.750    21  0.69    32  0.84  molprobity  1.000  
27  27    12   72.250    24  0.76    35  0.97  molprobity  1.000  
28  28    13  106.430    19  0.61    30  1.30  molprobity  1.000  
29  29    11  104.360    21  0.84    32  1.26  molprobity  1.000  
30  30    11   91.770    25  0.65    39  0.70  molprobity  1.000  
31  31    11   84.480    24  0.81    37  0.82  molprobity  1.000  
32  32    11   77.990    25  0.62    39  1.03  molprobity  1.000  
33  33    12   68.730    22  0.81    34  1.25  molprobity  1.000  
34  34    11   62.410    21  0.83    32  0.85  molprobity  1.000  
35  35    11   59.050    25  0.70    39  0.75  molprobity  1.000  
36  36    11   60.080    25  1.15    39  1.05  molprobity  1.000  
37  37    12   63.990    22  0.78    34  1.22  molprobity  1.000  
38  38    11   76.680    25  0.57    39  0.75  molprobity  1.000  
39  39    12   98.470    22  0.48    34  1.32  molprobity  1.000  
40  40    11  113.240    21  0.83    32  0.91  molprobity  1.000  
41  41    11  115.600    25  0.72    39  1.10  molprobity  1.000  
42  42    13  119.610    21  0.49    30  1.24  molprobity  1.000  
43  43     ?  165.260     ?     ?     ?     ?  ?           1.000  
44  44     ?  197.300     ?     ?     ?     ?  ?           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   2  OP2      1  0.41  2.03  
 2   2  H8       1  0.41  2.03  
 3  13  "H2'"    2  0.61  2.36  
 4  14  C8       2  0.61  2.36  
 5  16  "H2''"   3  0.61  2.35  
 6  17  C8       3  0.61  2.35  
 7  19  "H2'"    4  0.49  1.95  
 8  20  H72      4  0.49  1.95  
 9  24  "H2''"   5  0.52  2.09  
10  25  "H5'"    6  0.57  1.85  
11  25  OP1      5  0.52  2.09  
12  25  "H2'"    7  0.50  2.46  
13  26  "H2'"    8  0.70  2.26  
14  26  C6       7  0.50  2.46  
15  27  C8       8  0.70  2.26  
16  27  OP2      9  0.54  1.89  
17  27  H8       9  0.54  1.89  
18  29  "H5''"  10  0.58  1.68  
19  29  H6      10  0.58  1.68  
20  35  "H2''"   6  0.57  1.85  
21  36  "H2'"   11  0.47  2.49  
22  37  C6      11  0.47  2.49  
23  40  "H2'"   12  0.72  2.25  
24  41  C8      12  0.72  2.25  
25  41  "H2'"   13  0.58  2.38  
26  41  "H2''"  14  0.52  2.09  
27  42  C6      13  0.58  2.38  
28  42  "O5'"   14  0.52  2.09  
#
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  24  "O4'"  "C4'"  "C3'"  102.115  104.500  0.400  -5.96  
2  29  "O5'"  P      OP1    117.134  110.700  1.200   5.36  
#
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  0.956  0.066  -1.587  
 2   2  21  0.920  0.074  -1.515  
 3   3  21  0.912  0.075  -1.503  
 4   4  19  0.951  0.077  -1.455  
 5   5  22  0.947  0.080  -1.414  
 6   6  21  0.928  0.098  -1.213  
 7   7  19  0.951  0.073  -1.502  
 8   8  21  0.905  0.097  -1.225  
 9   9  19  0.957  0.078  -1.444  
10  10  21  0.934  0.111  -1.049  
11  11  22  0.941  0.095  -1.228  
12  12  21  0.949  0.095  -1.251  
13  13  19  0.941  0.104  -1.143  
14  14  22  0.948  0.085  -1.352  
15  15  21  0.958  0.076  -1.490  
16  16  19  0.954  0.073  -1.502  
17  17  22  0.955  0.087  -1.327  
18  18  21  0.942  0.079  -1.452  
19  19  19  0.942  0.102  -1.166  
20  20  20  0.952  0.087  -1.384  
21  21  19  0.920  0.083  -1.386  
22  22  20  0.944  0.107  -1.156  
23  23  19  0.958  0.101  -1.177  
24  24  20  0.959  0.100  -1.236  
25  25  20  0.952  0.113  -1.087  
26  26  19  0.950  0.084  -1.374  
27  27  22  0.935  0.102  -1.141  
28  28  17  0.947  0.157  -0.584  
29  29  19  0.927  0.082  -1.397  
30  30  22  0.917  0.099  -1.178  
31  31  21  0.915  0.104  -1.137  
32  32  22  0.932  0.077  -1.451  
33  33  20  0.961  0.085  -1.407  
34  34  19  0.969  0.083  -1.386  
35  35  22  0.959  0.087  -1.327  
36  36  22  0.967  0.086  -1.340  
37  37  20  0.947  0.094  -1.304  
38  38  22  0.939  0.082  -1.389  
39  39  20  0.920  0.109  -1.133  
40  40  19  0.914  0.103  -1.154  
41  41  22  0.913  0.090  -1.290  
42  42  20  0.910  0.137  -0.812  
43  43   1  0.833  0.067       ?  
44  44   1  0.841  0.073       ?  
#
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  
##
