data_6XDZ

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6XDZ
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6XDZ
_pdbx_vrpt_summary.PDB_deposition_date         2020-06-11
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-18
_pdbx_vrpt_summary.report_creation_date        2023-10-10:01:09
_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*CP*AP*G)-3')"  
2  polymer      "DNA (5'-D(P*AP*CP*AP*CP*CP*AP*CP*TP*CP*A)-3')"  
3  polymer      "DNA (5'-D(P*CP*TP*TP*GP*T)-3')"  
4  polymer      "DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*GP*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  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  3.106  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   28.19  141614     ?     ?  
2  2  1   60.90    1184  3.10  3.10  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1067  3.10  3.10  
5  1  3   46.99  130704     ?     ?  
6  2  3   85.23    1094  3.10  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  0.78  0.55  255  392  
2  1  2  B  B  0.81  0.56  222  338  
3  1  3  C  C  1.13  0.63  111  169  
4  1  4  D  D  0.91  0.53  368  568  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       9.75
_pdbx_vrpt_summary_geometry.num_H_reduce     477
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.55
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1467
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.88
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            41.172
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         129.472
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.24(3.11A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        5312
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.124
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.479
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.308
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.973
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.042;h,-h-k,-l:0.104;-k,-h,-l:0.075
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.24
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.11
_pdbx_vrpt_summary_diffraction.EDS_res_low               29.85
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[127.516,127.516,141.372,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.105
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 7.91% 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         5
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         92.58
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      292
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.50
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.11
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        29.85
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.23
#
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_clashes
 1  1  1  A   1  DG   A    1  .  ?        2  
 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  .  ?        ?  
 5  1  1  A   5  DA   A    5  .  ?        ?  
 6  1  1  A   6  DG   A    6  .  ?        1  
 7  1  1  A   7  DA   A    7  .  ?        1  
 8  1  1  A   8  DC   A    8  .  ?        ?  
 9  1  1  A   9  DC   A    9  .  ?        1  
10  1  1  A  10  DA   A   10  .  ?        1  
11  1  1  A  11  DG   A   11  .  ?        1  
12  1  2  B   1  DA   B   12  .  ?        ?  
13  1  2  B   2  DC   B   13  .  ?        ?  
14  1  2  B   3  DA   B   14  .  ?        ?  
15  1  2  B   4  DC   B   15  .  ?        ?  
16  1  2  B   5  DC   B   16  .  ?        1  
17  1  2  B   6  DA   B   17  .  ?        1  
18  1  2  B   7  DC   B   18  .  ?        1  
19  1  2  B   8  DT   B   19  .  ?        1  
20  1  2  B   9  DC   B   20  .  ?        ?  
21  1  2  B  10  DA   B   21  .  ?        ?  
22  1  3  C   1  DC   C    1  .  ?        ?  
23  1  3  C   2  DT   C    2  .  ?        ?  
24  1  3  C   3  DT   C    3  .  ?        1  
25  1  3  C   4  DG   C    4  .  ?        1  
26  1  3  C   5  DT   C    5  .  ?        ?  
27  1  4  D   1  DT   D    1  .  ?        ?  
28  1  4  D   2  DC   D    2  .  ?        ?  
29  1  4  D   3  DT   D    3  .  ?        1  
30  1  4  D   4  DG   D    4  .  ?        2  
31  1  4  D   5  DA   D    5  .  ?        1  
32  1  4  D   6  DG   D    6  .  ?        ?  
33  1  4  D   7  DT   D    7  .  ?        1  
34  1  4  D   8  DG   D    8  .  ?        1  
35  1  4  D   9  DG   D    9  .  ?        ?  
36  1  4  D  10  DG   D   10  .  ?        1  
37  1  4  D  11  DG   D   11  .  ?        1  
38  1  4  D  12  DT   D   12  .  ?        1  
39  1  4  D  13  DC   D   13  .  ?        ?  
40  1  4  D  14  DT   D   14  .  ?        ?  
41  1  4  D  15  DG   D   15  .  ?        1  
42  1  4  D  16  DC   D   16  .  ?        2  
43  1  5  E   .  CAC  C  101  .  ?        ?  
44  1  5  F   .  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  160.900    22  0.50    35  0.60  molprobity  1.000  
 2   2    11  159.760    24  0.49    37  0.55  molprobity  1.000  
 3   3    11  155.010    25  0.57    39  0.75  molprobity  1.000  
 4   4    11  163.650    21  0.64    32  0.87  molprobity  1.000  
 5   5    11  163.120    24  0.43    37  0.65  molprobity  1.000  
 6   6    11  159.900    25  0.46    39  0.71  molprobity  1.000  
 7   7    11  159.710    24  0.45    37  0.67  molprobity  1.000  
 8   8    11  159.970    21  0.69    32  1.03  molprobity  1.000  
 9   9    11  147.390    21  0.57    32  0.90  molprobity  1.000  
10  10    11  135.330    24  0.73    37  1.12  molprobity  1.000  
11  11    12  122.680    24  0.45    35  0.56  molprobity  1.000  
12  12    11  123.560    24  0.54    37  0.76  molprobity  1.000  
13  13    11  119.240    21  0.73    32  0.89  molprobity  1.000  
14  14    11  113.570    24  0.59    37  0.61  molprobity  1.000  
15  15    11  114.060    21  0.63    32  0.82  molprobity  1.000  
16  16    11  119.960    21  0.48    32  0.78  molprobity  1.000  
17  17    11  125.350    24  0.56    37  0.75  molprobity  1.000  
18  18    11  127.090    21  0.67    32  0.81  molprobity  1.000  
19  19    12  140.440    22  0.49    34  1.21  molprobity  1.000  
20  20    11  151.060    21  0.38    32  0.75  molprobity  1.000  
21  21    12  161.210    23  0.41    33  0.59  molprobity  1.000  
22  22    11   97.630    21  0.71    32  0.67  molprobity  1.000  
23  23    12   91.420    22  0.61    34  1.37  molprobity  1.000  
24  24    12   89.030    22  0.64    34  1.33  molprobity  1.000  
25  25    11   97.180    25  0.56    39  0.73  molprobity  1.000  
26  26    13  104.160    21  0.63    30  1.38  molprobity  1.000  
27  27    13  160.300    19  0.45    30  1.18  molprobity  1.000  
28  28    11  164.010    21  0.40    32  0.66  molprobity  1.000  
29  29    12  169.440    22  0.51    34  1.40  molprobity  1.000  
30  30    11  160.340    25  0.42    39  0.72  molprobity  1.000  
31  31    11  154.960    24  0.40    37  0.60  molprobity  1.000  
32  32    11  133.910    25  0.53    39  0.77  molprobity  1.000  
33  33    12  119.080    22  0.53    34  1.29  molprobity  1.000  
34  34    11   98.640    25  0.67    39  0.69  molprobity  1.000  
35  35    11   90.920    25  0.56    39  0.69  molprobity  1.000  
36  36    11  103.140    25  0.58    39  0.72  molprobity  1.000  
37  37    11  116.900    25  0.50    39  0.71  molprobity  1.000  
38  38    12  133.750    22  0.40    34  1.18  molprobity  1.000  
39  39    11  148.520    21  0.40    32  0.77  molprobity  1.000  
40  40    12  170.420    22  0.56    34  1.23  molprobity  1.000  
41  41    11  173.980    25  0.83    39  0.84  molprobity  1.000  
42  42    12  167.910    20  0.37    28  0.54  molprobity  1.000  
43  43     ?  190.340     ?     ?     ?     ?  ?           1.000  
44  44     ?  132.320     ?     ?     ?     ?  ?           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  N3       1  0.41  2.35  
 2   1  "H2'"    1  0.41  2.35  
 3   3  H1       2  0.43  1.66  
 4   6  "H2''"   3  0.40  2.21  
 5   7  "O4'"    3  0.40  2.21  
 6   9  H42      4  0.63  1.46  
 7  10  "H2''"   5  0.51  2.10  
 8  11  "O5'"    5  0.51  2.10  
 9  16  "H2''"   6  0.50  2.47  
10  17  C8       6  0.50  2.47  
11  18  "H2'"    7  0.40  2.03  
12  19  H72      7  0.40  2.03  
13  24  "H2'"    8  0.49  2.47  
14  25  C8       8  0.49  2.47  
15  29  "H2''"   9  0.53  2.42  
16  30  C8       9  0.53  2.42  
17  30  "H2''"  10  0.52  2.46  
18  31  C8      10  0.52  2.46  
19  33  "H2''"  11  0.66  2.31  
20  34  C8      11  0.66  2.31  
21  36  H1       4  0.63  1.46  
22  37  "H2'"   12  0.46  2.51  
23  38  C6      12  0.46  2.51  
24  41  "H4'"   13  0.45  2.16  
25  42  OP1     13  0.45  2.16  
26  42  H42      2  0.43  1.66  
#
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  0.904  0.092  -1.265  
 2   2  21  0.923  0.076  -1.490  
 3   3  22  0.896  0.080  -1.414  
 4   4  19  0.935  0.096  -1.235  
 5   5  21  0.932  0.090  -1.314  
 6   6  22  0.935  0.080  -1.414  
 7   7  21  0.904  0.082  -1.414  
 8   8  19  0.943  0.130  -0.841  
 9   9  19  0.895  0.118  -0.980  
10  10  21  0.950  0.109  -1.074  
11  11  22  0.926  0.095  -1.228  
12  12  21  0.935  0.118  -0.961  
13  13  19  0.952  0.112  -1.050  
14  14  21  0.959  0.085  -1.377  
15  15  19  0.962  0.084  -1.374  
16  16  19  0.957  0.073  -1.502  
17  17  21  0.947  0.098  -1.213  
18  18  19  0.954  0.103  -1.154  
19  19  20  0.949  0.125  -0.950  
20  20  19  0.972  0.084  -1.374  
21  21  21  0.957  0.112  -1.037  
22  22  19  0.927  0.138  -0.749  
23  23  20  0.960  0.149  -0.675  
24  24  20  0.957  0.134  -0.847  
25  25  22  0.931  0.091  -1.278  
26  26  20  0.927  0.132  -0.870  
27  27  17  0.957  0.101  -1.224  
28  28  19  0.876  0.094  -1.258  
29  29  20  0.912  0.107  -1.156  
30  30  22  0.936  0.071  -1.525  
31  31  21  0.942  0.072  -1.540  
32  32  22  0.947  0.082  -1.389  
33  33  20  0.959  0.087  -1.384  
34  34  22  0.966  0.098  -1.191  
35  35  22  0.944  0.138  -0.695  
36  36  22  0.949  0.111  -1.030  
37  37  22  0.956  0.083  -1.377  
38  38  20  0.913  0.122  -0.984  
39  39  19  0.891  0.104  -1.143  
40  40  20  0.930  0.101  -1.224  
41  41  22  0.892  0.087  -1.327  
42  42  19  0.925  0.071  -1.525  
43  43   1  0.982  0.033       ?  
44  44   1  0.972  0.166       ?  
#
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  
##
