data_7ZQL

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7ZQL
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7ZQL
_pdbx_vrpt_summary.PDB_deposition_date         2022-05-01
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2023-03-08
_pdbx_vrpt_summary.report_creation_date        2023-03-02:15:07
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,buster-report,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   Y
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')"  
2  non-polymer  "MAGNESIUM ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  3  
E  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  2.55  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   25.75  141614     ?     ?  
2  2  1   31.53    1332  2.52  2.56  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1272  2.52  2.56  
5  1  3   57.97  130704     ?     ?  
6  2  3   85.39    1284  2.52  2.56  
#
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  1  B  100.00  
4  4  2  B  1  1  B  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  1.24  0.64  272  418  
2  1  1  B  B  1.23  0.64  272  418  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       10.54
_pdbx_vrpt_summary_geometry.num_H_reduce     272
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   544
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.64
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  836
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.23
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 119.285
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            16.288
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         32.464
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.89(2.56A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1899
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.264
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.256
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.466
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.302
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.944
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.23
_pdbx_vrpt_summary_diffraction.EDS_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.55
_pdbx_vrpt_summary_diffraction.EDS_res_low               17.91
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[44.110,31.017,19.763,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.770
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 10.81% 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         1
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         79.05
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      211
_pdbx_vrpt_summary_diffraction.percent_free_reflections  11.11
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.55
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        17.92
_pdbx_vrpt_summary_diffraction.PDB_R                     0.18
_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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A   1  DC   A    1  .  ?        ?     ?  ?     
 2  1  1  A   2  DG   A    2  .  ?        ?     ?  ?     
 3  1  1  A   3  DC   A    3  .  ?        ?     ?  ?     
 4  1  1  A   4  DG   A    4  .  ?        ?     ?  ?     
 5  1  1  A   5  DA   A    5  .  ?        ?     ?  ?     
 6  1  1  A   6  DA   A    6  .  ?        ?     3  ?     
 7  1  1  A   7  DT   A    7  .  ?        ?     3  ?     
 8  1  1  A   8  DT   A    8  .  ?        ?     ?  ?     
 9  1  1  A   9  DC   A    9  .  ?        ?     ?  ?     
10  1  1  A  10  DG   A   10  .  ?        ?     ?  ?     
11  1  1  A  11  DC   A   11  .  ?        1     1  ?     
12  1  1  A  12  DG   A   12  .  ?        ?     ?  ?     
13  1  1  B   1  DC   B   13  .  ?        ?     1  ?     
14  1  1  B   2  DG   B   14  .  ?        ?     1  ?     
15  1  1  B   3  DC   B   15  .  ?        ?     ?  ?     
16  1  1  B   4  DG   B   16  .  ?        ?     1  ?     
17  1  1  B   5  DA   B   17  .  ?        ?     ?  ?     
18  1  1  B   6  DA   B   18  .  ?        ?     1  ?     
19  1  1  B   7  DT   B   19  .  ?        ?     1  ?     
20  1  1  B   8  DT   B   20  .  ?        ?     ?  ?     
21  1  1  B   9  DC   B   21  .  ?        ?     ?  ?     
22  1  1  B  10  DG   B   22  .  ?        ?     ?  ?     
23  1  1  B  11  DC   B   23  .  ?        ?     1  ?     
24  1  1  B  12  DG   B   24  .  ?        ?     1  ?     
25  1  2  C   .  MG   A  101  .  ?        ?     ?  Y     
26  1  3  D   .  HOH  A  201  .  ?        ?     1  ?     
27  1  3  D   .  HOH  A  202  .  ?        ?     ?  ?     
28  1  3  D   .  HOH  A  203  .  ?        ?     ?  ?     
29  1  3  D   .  HOH  A  204  .  ?        ?     ?  ?     
30  1  3  D   .  HOH  A  205  .  ?        ?     ?  ?     
31  1  3  D   .  HOH  A  206  .  ?        ?     ?  ?     
32  1  3  D   .  HOH  A  207  .  ?        ?     ?  ?     
33  1  3  D   .  HOH  A  208  .  ?        ?     ?  ?     
34  1  3  D   .  HOH  A  209  .  ?        ?     ?  ?     
35  1  3  D   .  HOH  A  210  .  ?        ?     ?  ?     
36  1  3  D   .  HOH  A  211  .  ?        ?     ?  ?     
37  1  3  E   .  HOH  B  101  .  ?        ?     ?  ?     
38  1  3  E   .  HOH  B  102  .  ?        ?     ?  ?     
39  1  3  E   .  HOH  B  103  .  ?        ?     ?  ?     
40  1  3  E   .  HOH  B  104  .  ?        ?     ?  ?     
41  1  3  E   .  HOH  B  105  .  ?        ?     ?  ?     
42  1  3  E   .  HOH  B  106  .  ?        ?     ?  ?     
43  1  3  E   .  HOH  B  107  .  ?        ?     ?  ?     
44  1  3  E   .  HOH  B  108  .  ?        ?     1  ?     
#
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  24.610    18  0.63    28  1.08  molprobity  1.000  
 2   2    11  24.970    25  0.56    39  1.06  molprobity  1.000  
 3   3    11  21.340    21  0.77    32  1.21  molprobity  1.000  
 4   4    11  20.640    25  0.91    39  1.34  molprobity  1.000  
 5   5    11  21.600    24  0.57    37  1.10  molprobity  1.000  
 6   6    11  16.130    24  0.58    37  1.26  molprobity  1.000  
 7   7    12  18.880    22  0.35    34  1.18  molprobity  1.000  
 8   8    12  19.690    22  0.52    34  1.26  molprobity  1.000  
 9   9    11  19.440    21  0.67    32  1.28  molprobity  1.000  
10  10    11  23.150    25  0.57    39  1.50  molprobity  1.000  
11  11    11  28.710    21  0.71    32  1.45  molprobity  1.000  
12  12    12  34.340    24  0.61    35  1.01  molprobity  1.000  
13  13    12  35.190    18  0.70    28  1.25  molprobity  1.000  
14  14    11  23.590    25  0.57    39  1.02  molprobity  1.000  
15  15    11  19.150    21  0.76    32  1.55  molprobity  1.000  
16  16    11  16.130    25  0.50    39  1.16  molprobity  1.000  
17  17    11  17.980    24  0.65    37  1.08  molprobity  1.000  
18  18    11  18.990    24  0.56    37  1.16  molprobity  1.000  
19  19    12  21.580    22  0.42    34  1.08  molprobity  1.000  
20  20    12  23.520    22  0.44    34  1.26  molprobity  1.000  
21  21    11  29.060    21  1.00    32  1.36  molprobity  1.000  
22  22    11  27.750    25  0.63    39  1.51  molprobity  1.000  
23  23    11  27.080    21  0.76    32  1.32  molprobity  1.000  
24  24    12  19.640    24  0.55    35  0.88  molprobity  1.000  
25  25     ?  28.190     ?     ?     ?     ?  ?           1.000  
26  26     ?  17.570     ?     ?     ?     ?  ?           1.000  
27  27     ?  10.720     ?     ?     ?     ?  ?           1.000  
28  28     ?  16.180     ?     ?     ?     ?  ?           1.000  
29  29     ?  16.360     ?     ?     ?     ?  ?           1.000  
30  30     ?  10.610     ?     ?     ?     ?  ?           1.000  
31  31     ?  14.840     ?     ?     ?     ?  ?           1.000  
32  32     ?  24.450     ?     ?     ?     ?  ?           1.000  
33  33     ?  22.700     ?     ?     ?     ?  ?           1.000  
34  34     ?  22.270     ?     ?     ?     ?  ?           1.000  
35  35     ?  17.780     ?     ?     ?     ?  ?           1.000  
36  36     ?  28.680     ?     ?     ?     ?  ?           1.000  
37  37     ?  14.300     ?     ?     ?     ?  ?           1.000  
38  38     ?  25.780     ?     ?     ?     ?  ?           1.000  
39  39     ?  15.390     ?     ?     ?     ?  ?           1.000  
40  40     ?  15.110     ?     ?     ?     ?  ?           1.000  
41  41     ?  18.240     ?     ?     ?     ?  ?           1.000  
42  42     ?  23.700     ?     ?     ?     ?  ?           1.000  
43  43     ?  16.240     ?     ?     ?     ?  ?           1.000  
44  44     ?  26.550     ?     ?     ?     ?  ?           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   6  "H2''"  1  0.53  1.90  
 2   6  "H2''"  2  0.45  2.47  
 3   6  "H1'"   3  0.52  1.91  
 4   7  "H5'"   1  0.53  1.90  
 5   7  "H5''"  3  0.52  1.91  
 6   7  "C5'"   2  0.45  2.47  
 7  11  OP2     4  0.48  2.20  
 8  13  "H2''"  5  0.44  2.53  
 9  14  C8      5  0.44  2.53  
10  16  "H2'"   6  0.51  2.10  
11  18  "H2''"  7  0.54  1.90  
12  19  "H5'"   7  0.54  1.90  
13  23  "H2''"  8  0.47  2.49  
14  24  C8      8  0.47  2.49  
15  26  O       4  0.48  2.20  
16  44  O       6  0.51  2.10  
#
_pdbx_vrpt_instance_intra_angle_outliers.ordinal      1
_pdbx_vrpt_instance_intra_angle_outliers.instance_id  11
_pdbx_vrpt_instance_intra_angle_outliers.atom_1       P
_pdbx_vrpt_instance_intra_angle_outliers.atom_2       "O3'"
_pdbx_vrpt_instance_intra_angle_outliers.atom_3       "C3'"
_pdbx_vrpt_instance_intra_angle_outliers.obs          113.029
_pdbx_vrpt_instance_intra_angle_outliers.mean         119.700
_pdbx_vrpt_instance_intra_angle_outliers.stdev        1.200
_pdbx_vrpt_instance_intra_angle_outliers.Z            -5.56
_pdbx_vrpt_instance_intra_angle_outliers.link         Y
#
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  16  0.950  0.126  -0.604  
 2   2  22  0.939  0.137  -0.401  
 3   3  19  0.961  0.133  -0.488  
 4   4  22  0.950  0.121  -0.683  
 5   5  21  0.961  0.107  -0.907  
 6   6  21  0.970  0.092  -1.136  
 7   7  20  0.973  0.092  -1.120  
 8   8  20  0.955  0.122  -0.696  
 9   9  19  0.957  0.124  -0.637  
10  10  22  0.950  0.116  -0.771  
11  11  19  0.946  0.133  -0.488  
12  12  22  0.923  0.179   0.338  
13  13  16  0.935  0.180   0.287  
14  14  22  0.938  0.113  -0.824  
15  15  19  0.965  0.102  -1.000  
16  16  22  0.942  0.135  -0.437  
17  17  21  0.959  0.105  -0.938  
18  18  21  0.959  0.109  -0.877  
19  19  20  0.954  0.116  -0.781  
20  20  20  0.954  0.114  -0.809  
21  21  19  0.961  0.123  -0.653  
22  22  22  0.942  0.141  -0.331  
23  23  19  0.954  0.126  -0.604  
24  24  22  0.935  0.153  -0.120  
25  25   1  0.977  0.059       ?  
26  26   1  0.958  0.205       ?  
27  27   1  0.866  0.231       ?  
28  28   1  0.912  0.153       ?  
29  29   1  0.766  0.233       ?  
30  30   1  0.908  0.274       ?  
31  31   1  0.660  0.428       ?  
32  32   1  0.363  0.395       ?  
33  33   1  0.533  0.392       ?  
34  34   1  0.892  0.441       ?  
35  35   1  0.702  0.282       ?  
36  36   1  0.930  0.114       ?  
37  37   1  0.930  0.235       ?  
38  38   1  0.880  0.632       ?  
39  39   1  0.930  0.277       ?  
40  40   1  0.969  0.146       ?  
41  41   1  0.770  0.273       ?  
42  42   1  0.844  0.227       ?  
43  43   1  0.875  0.358       ?  
44  44   1  0.831  0.604       ?  
#
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          2.32.1                                                                Y  
4  dcc          "2.26  (2020-01-20)"                                                  Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
