data_6XO9

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6XO9
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6XO9
_pdbx_vrpt_summary.PDB_deposition_date         2020-07-06
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-18
_pdbx_vrpt_summary.report_creation_date        2023-10-10:02:12
_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*TP*TP*GP*A)-3')"  
2  polymer      "DNA (5'-D(P*CP*GP*AP*GP*AP*CP*TP*CP*A)-3')"  
3  polymer      "DNA (5'-D(P*TP*CP*AP*TP*CP*G)-3')"  
4  polymer      "DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*CP*AP*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  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  3.103  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   51.69    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  1.00  0.92  278  428  
2  1  2  B  B  0.94  0.91  206  315  
3  1  3  C  C  1.22  1.32  134  204  
4  1  4  D  D  1.08  0.94  338  520  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       12.74
_pdbx_vrpt_summary_geometry.num_H_reduce     478
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.99
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1467
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.05
#
_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         103.610
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.68(3.12A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        4498
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.072
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.484
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.312
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.967
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.041;h,-h-k,-l:0.065;-k,-h,-l:0.086
_pdbx_vrpt_summary_diffraction.DCC_R                     0.24
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.26
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.10
_pdbx_vrpt_summary_diffraction.EDS_res_low               34.19
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[102.864,102.864,135.504,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.287
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 6.81% 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         15
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         78.54
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      461
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.25
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.10
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        34.20
_pdbx_vrpt_summary_diffraction.PDB_R                     0.24
_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_bond_outliers
_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  .  ?        ?     ?     ?  
 3  1  1  A   3  DG   A    3  .  ?        ?     ?     ?  
 4  1  1  A   4  DC   A    4  .  ?        ?     ?     1  
 5  1  1  A   5  DA   A    5  .  ?        ?     ?     ?  
 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  DT   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  .  ?        ?     ?     2  
13  1  2  B   1  DC   B   12  .  ?        ?     ?     ?  
14  1  2  B   2  DG   B   13  .  ?        ?     ?     ?  
15  1  2  B   3  DA   B   14  .  ?        ?     ?     2  
16  1  2  B   4  DG   B   15  .  ?        ?     ?     2  
17  1  2  B   5  DA   B   16  .  ?        ?     ?     1  
18  1  2  B   6  DC   B   17  .  ?        ?     ?     2  
19  1  2  B   7  DT   B   18  .  ?        ?     ?     4  
20  1  2  B   8  DC   B   19  .  ?        ?     ?     ?  
21  1  2  B   9  DA   B   20  .  ?        ?     ?     ?  
22  1  3  C   1  DT   C    0  .  ?        ?     ?     ?  
23  1  3  C   2  DC   C    1  .  ?        ?     ?     ?  
24  1  3  C   3  DA   C    2  .  ?        ?     ?     ?  
25  1  3  C   4  DT   C    3  .  ?        1     1     2  
26  1  3  C   5  DC   C    4  .  ?        ?     1     1  
27  1  3  C   6  DG   C    5  .  ?        ?     ?     1  
28  1  4  D   1  DT   D    2  .  ?        ?     ?     1  
29  1  4  D   2  DC   D    3  .  ?        ?     ?     1  
30  1  4  D   3  DT   D    4  .  ?        ?     ?     2  
31  1  4  D   4  DG   D    5  .  ?        ?     ?     4  
32  1  4  D   5  DA   D    6  .  ?        ?     ?     ?  
33  1  4  D   6  DG   D    7  .  ?        ?     ?     1  
34  1  4  D   7  DT   D    8  .  ?        ?     ?     ?  
35  1  4  D   8  DC   D    9  .  ?        ?     ?     ?  
36  1  4  D   9  DA   D   10  .  ?        ?     ?     2  
37  1  4  D  10  DG   D   11  .  ?        ?     ?     ?  
38  1  4  D  11  DT   D   12  .  ?        ?     ?     ?  
39  1  4  D  12  DC   D   13  .  ?        ?     ?     1  
40  1  4  D  13  DT   D   14  .  ?        ?     ?     1  
41  1  4  D  14  DG   D   15  .  ?        ?     ?     1  
42  1  4  D  15  DC   D   16  .  ?        ?     ?     ?  
43  1  5  E   .  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  133.450    22  1.77    35  1.50  molprobity  1.000  
 2   2    11  137.680    24  0.77    37  0.82  molprobity  1.000  
 3   3    11  138.040    25  0.80    39  0.72  molprobity  1.000  
 4   4    11  142.780    21  0.93    32  1.00  molprobity  1.000  
 5   5    11  143.360    24  0.70    37  0.62  molprobity  1.000  
 6   6    11  141.810    25  1.01    39  0.76  molprobity  1.000  
 7   7    11  136.420    24  0.70    37  0.72  molprobity  1.000  
 8   8    11  127.280    21  0.49    32  1.15  molprobity  1.000  
 9   9    12  115.070    22  0.49    34  1.48  molprobity  1.000  
10  10    12  117.290    22  0.87    34  1.23  molprobity  1.000  
11  11    11  108.730    25  0.94    39  0.83  molprobity  1.000  
12  12    12  102.330    23  0.91    33  0.78  molprobity  1.000  
13  13    11  101.170    21  0.98    32  1.07  molprobity  1.000  
14  14    11  103.640    25  0.93    39  1.04  molprobity  1.000  
15  15    11  103.210    24  1.12    37  0.72  molprobity  1.000  
16  16    11  106.290    25  0.84    39  0.59  molprobity  1.000  
17  17    11  107.400    24  0.97    37  0.92  molprobity  1.000  
18  18    11   98.160    21  0.67    32  0.84  molprobity  1.000  
19  19    12  104.960    22  0.74    34  1.53  molprobity  1.000  
20  20    11  121.640    21  0.77    32  0.93  molprobity  1.000  
21  21    12  129.350    23  0.99    33  0.50  molprobity  1.000  
22  22    12  102.820    22  0.64    34  1.24  molprobity  1.000  
23  23    11  100.320    21  1.10    32  0.95  molprobity  1.000  
24  24    11   97.260    24  1.30    37  0.84  molprobity  1.000  
25  25    12   91.630    22  2.15    34  1.92  molprobity  1.000  
26  26    11  101.350    21  1.26    32  1.36  molprobity  1.000  
27  27    12  101.910    24  1.00    35  0.61  molprobity  1.000  
28  28    13  134.390    19  0.47    30  1.33  molprobity  1.000  
29  29    11  132.940    21  0.81    32  1.25  molprobity  1.000  
30  30    12  135.500    22  0.97    34  1.59  molprobity  1.000  
31  31    11  125.840    25  1.05    39  0.81  molprobity  1.000  
32  32    11  117.570    24  1.05    37  0.84  molprobity  1.000  
33  33    11  106.080    25  1.35    39  0.91  molprobity  1.000  
34  34    12   93.480    22  0.86    34  1.28  molprobity  1.000  
35  35    11   89.190    21  1.11    32  1.09  molprobity  1.000  
36  36    11  103.110    24  1.16    37  0.73  molprobity  1.000  
37  37    11  107.820    25  1.17    39  0.69  molprobity  1.000  
38  38    12  118.290    22  0.70    34  1.33  molprobity  1.000  
39  39    11  141.710    21  0.67    32  0.81  molprobity  1.000  
40  40    12  169.540    22  0.62    34  1.29  molprobity  1.000  
41  41    11  162.480    25  0.87    39  0.98  molprobity  1.000  
42  42    12  151.800    20  0.48    28  0.86  molprobity  1.000  
43  43     ?  128.630     ?     ?     ?     ?  ?           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   4  H42      1  0.70  1.37  
 2   9  "H2''"   2  0.56  1.88  
 3  10  "H5'"    2  0.56  1.88  
 4  12  H8       3  0.52  1.92  
 5  12  OP2      3  0.52  1.92  
 6  15  "H2''"   4  0.56  1.87  
 7  15  "H2'"    5  0.47  2.50  
 8  16  "H5'"    4  0.56  1.87  
 9  16  C8       5  0.47  2.50  
10  17  "H1'"    6  0.45  1.98  
11  18  H42      7  0.50  1.59  
12  18  "H5''"   6  0.45  1.98  
13  19  C6       8  0.41  2.55  
14  19  "H5'"    8  0.41  2.55  
15  19  "H5'"    9  0.41  1.85  
16  19  H6       9  0.41  1.85  
17  25  O2      10  0.56  2.06  
18  25  "H2'"   10  0.56  2.06  
19  26  "H2''"  11  0.51  1.92  
20  27  "H5'"   11  0.51  1.92  
21  28  "H2''"  12  0.52  2.10  
22  29  O2      12  0.52  2.10  
23  30  "H2''"  13  0.59  1.83  
24  30  "C2'"   14  0.44  2.47  
25  31  "H5'"   13  0.59  1.83  
26  31  "H5'"   14  0.44  2.47  
27  31  OP2     15  0.50  2.10  
28  31  "H2'"   15  0.50  2.10  
29  33  H1       7  0.50  1.59  
30  36  "H5''"  16  0.48  1.78  
31  36  H8      16  0.48  1.78  
32  39  "H2''"  17  0.61  1.81  
33  40  "H5''"  17  0.61  1.81  
34  41  H1       1  0.70  1.37  
#
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   1  "C3'"  "O3'"  1.507  1.435  0.013  5.54  
2  25  "C1'"  N1     1.578  1.488  0.013  6.90  
#
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  25  N3     C4     O4     122.986  119.900  0.600   5.14  
2  26  "C1'"  "O4'"  "C4'"  105.042  110.100  1.000  -5.06  
#
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  0.891  0.122  -0.893  
 2   2  21  0.895  0.084  -1.389  
 3   3  22  0.921  0.092  -1.265  
 4   4  19  0.942  0.083  -1.386  
 5   5  21  0.911  0.096  -1.238  
 6   6  22  0.925  0.079  -1.426  
 7   7  21  0.912  0.077  -1.477  
 8   8  19  0.929  0.091  -1.293  
 9   9  20  0.911  0.104  -1.190  
10  10  20  0.933  0.088  -1.373  
11  11  22  0.941  0.097  -1.203  
12  12  21  0.954  0.087  -1.351  
13  13  19  0.939  0.086  -1.351  
14  14  22  0.968  0.068  -1.563  
15  15  21  0.970  0.053  -1.780  
16  16  22  0.936  0.073  -1.501  
17  17  21  0.928  0.080  -1.440  
18  18  19  0.920  0.113  -1.038  
19  19  20  0.926  0.104  -1.190  
20  20  19  0.948  0.092  -1.282  
21  21  21  0.952  0.095  -1.251  
22  22  20  0.935  0.113  -1.087  
23  23  19  0.951  0.104  -1.143  
24  24  21  0.955  0.115  -0.999  
25  25  20  0.964  0.120  -1.007  
26  26  19  0.966  0.079  -1.432  
27  27  22  0.935  0.090  -1.290  
28  28  17  0.949  0.090  -1.350  
29  29  19  0.879  0.099  -1.200  
30  30  20  0.889  0.089  -1.362  
31  31  22  0.925  0.081  -1.401  
32  32  21  0.957  0.062  -1.666  
33  33  22  0.937  0.087  -1.327  
34  34  20  0.934  0.103  -1.201  
35  35  19  0.948  0.150  -0.610  
36  36  21  0.943  0.111  -1.049  
37  37  22  0.957  0.079  -1.426  
38  38  20  0.948  0.090  -1.350  
39  39  19  0.845  0.088  -1.328  
40  40  20  0.893  0.095  -1.293  
41  41  22  0.860  0.087  -1.327  
42  42  19  0.863  0.106  -1.119  
43  43   1  0.939  0.190       ?  
#
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  
##
