data_5WSP

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  5WSP
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    5WSP
_pdbx_vrpt_summary.PDB_deposition_date         2016-12-08
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2024-03-20
_pdbx_vrpt_summary.report_creation_date        2024-03-13:09:44
_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*GP*TP*CP*GP*TP*CP*C)-3')"  
2  non-polymer  "STRONTIUM ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  1.502  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   65.78  141614     ?     ?  
2  2  1   51.78    3144  1.50  1.50  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    2884  1.50  1.50  
5  1  3   84.49  130704     ?     ?  
6  2  3   55.17    2936  1.50  1.50  
#
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  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     A
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      1.04
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.09
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   178
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  273
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.95
_pdbx_vrpt_summary_geometry.num_H_reduce     92
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   178
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.09
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  273
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.04
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 109.330
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            43.711
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         12.828
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.64(1.50A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3932
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.268
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.346
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.469
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.304
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.958
_pdbx_vrpt_summary_diffraction.DCC_R                     0.18
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.20
_pdbx_vrpt_summary_diffraction.EDS_R                     0.19
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.50
_pdbx_vrpt_summary_diffraction.EDS_res_low               21.64
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[12.827,12.827,12.829,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.000
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 16.10% 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         0
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         98.94
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      228
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.80
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.50
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        21.64
_pdbx_vrpt_summary_diffraction.PDB_R                     0.19
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.20
#
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  1  1  A  2  DG   A    2  .  ?        ?  
 3  1  1  A  3  DT   A    3  .  ?        1  
 4  1  1  A  4  DC   A    4  .  ?        1  
 5  1  1  A  5  DG   A    5  .  ?        ?  
 6  1  1  A  6  DT   A    6  .  ?        ?  
 7  1  1  A  7  DC   A    7  .  ?        ?  
 8  1  1  A  8  DC   A    8  .  ?        ?  
 9  1  2  B  .  SR   A  101  .  ?        ?  
10  1  3  C  .  HOH  A  201  .  ?        ?  
11  1  3  C  .  HOH  A  202  .  ?        ?  
12  1  3  C  .  HOH  A  203  .  ?        ?  
13  1  3  C  .  HOH  A  204  .  ?        ?  
14  1  3  C  .  HOH  A  205  .  ?        ?  
15  1  3  C  .  HOH  A  206  .  ?        ?  
16  1  3  C  .  HOH  A  207  .  ?        ?  
17  1  3  C  .  HOH  A  208  .  ?        ?  
18  1  3  C  .  HOH  A  209  .  ?        ?  
19  1  3  C  .  HOH  A  210  .  ?        ?  
20  1  3  C  .  HOH  A  211  .  ?        ?  
21  1  3  C  .  HOH  A  212  .  ?        ?  
22  1  3  C  .  HOH  A  213  .  ?        ?  
23  1  3  C  .  HOH  A  214  .  ?        ?  
24  1  3  C  .  HOH  A  215  .  ?        ?  
25  1  3  C  .  HOH  A  216  .  ?        ?  
26  1  3  C  .  HOH  A  217  .  ?        ?  
27  1  3  C  .  HOH  A  218  .  ?        ?  
28  1  3  C  .  HOH  A  219  .  ?        ?  
29  1  3  C  .  HOH  A  220  .  ?        ?  
30  1  3  C  .  HOH  A  221  .  ?        ?  
31  1  3  C  .  HOH  A  222  .  ?        ?  
32  1  3  C  .  HOH  A  223  .  ?        ?  
33  1  3  C  .  HOH  A  224  .  ?        ?  
34  1  3  C  .  HOH  A  225  .  ?        ?  
35  1  3  C  .  HOH  A  226  .  ?        ?  
36  1  3  C  .  HOH  A  227  .  ?        ?  
37  1  3  C  .  HOH  A  228  .  ?        ?  
38  1  3  C  .  HOH  A  229  .  ?        ?  
39  1  3  C  .  HOH  A  230  .  ?        ?  
40  1  3  C  .  HOH  A  231  .  ?        ?  
41  1  3  C  .  HOH  A  232  .  ?        ?  
42  1  3  C  .  HOH  A  233  .  ?        ?  
43  1  3  C  .  HOH  A  234  .  ?        ?  
44  1  3  C  .  HOH  A  235  .  ?        ?  
45  1  3  C  .  HOH  A  236  .  ?        ?  
46  1  3  C  .  HOH  A  237  .  ?        ?  
47  1  3  C  .  HOH  A  238  .  ?        ?  
48  1  3  C  .  HOH  A  239  .  ?        ?  
49  1  3  C  .  HOH  A  240  .  ?        ?  
50  1  3  C  .  HOH  A  241  .  ?        ?  
51  1  3  C  .  HOH  A  242  .  ?        ?  
52  1  3  C  .  HOH  A  243  .  ?        ?  
53  1  3  C  .  HOH  A  244  .  ?        ?  
54  1  3  C  .  HOH  A  245  .  ?        ?  
55  1  3  C  .  HOH  A  246  .  ?        ?  
56  1  3  C  .  HOH  A  247  .  ?        ?  
57  1  3  C  .  HOH  A  248  .  ?        ?  
58  1  3  C  .  HOH  A  249  .  ?        ?  
59  1  3  C  .  HOH  A  250  .  ?        ?  
60  1  3  C  .  HOH  A  251  .  ?        ?  
61  1  3  C  .  HOH  A  252  .  ?        ?  
62  1  3  C  .  HOH  A  253  .  ?        ?  
63  1  3  C  .  HOH  A  254  .  ?        ?  
64  1  3  C  .  HOH  A  255  .  ?        ?  
65  1  3  C  .  HOH  A  256  .  ?        ?  
66  1  3  C  .  HOH  A  257  .  ?        ?  
67  1  3  C  .  HOH  A  258  .  ?        ?  
68  1  3  C  .  HOH  A  259  .  ?        ?  
69  1  3  C  .  HOH  A  260  .  ?        ?  
70  1  3  C  .  HOH  A  261  .  ?        ?  
71  1  3  C  .  HOH  A  262  .  ?        ?  
72  1  3  C  .  HOH  A  263  .  ?        ?  
73  1  3  C  .  HOH  A  264  .  ?        ?  
74  1  3  C  .  HOH  A  265  .  ?        ?  
#
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  13.320    22  1.21    35  0.94  molprobity  1.000  
 2   2    11  15.140    25  1.24    39  0.93  molprobity  1.000  
 3   3    12  12.980    22  1.18    34  1.35  molprobity  1.000  
 4   4    11  14.220    21  0.85    32  0.93  molprobity  1.000  
 5   5    11  12.760    25  1.15    39  0.95  molprobity  1.000  
 6   6    12  14.230    22  0.81    34  1.22  molprobity  1.000  
 7   7    11  15.510    21  0.96    32  1.01  molprobity  1.000  
 8   8    12  17.700    20  1.22    28  0.85  molprobity  1.000  
 9   9     ?  14.430     ?     ?     ?     ?  ?           0.390  
10  10     ?  23.410     ?     ?     ?     ?  ?           1.000  
11  11     ?  27.450     ?     ?     ?     ?  ?           1.000  
12  12     ?  36.180     ?     ?     ?     ?  ?           1.000  
13  13     ?  25.710     ?     ?     ?     ?  ?           1.000  
14  14     ?  18.640     ?     ?     ?     ?  ?           1.000  
15  15     ?  18.370     ?     ?     ?     ?  ?           1.000  
16  16     ?  31.100     ?     ?     ?     ?  ?           1.000  
17  17     ?  29.080     ?     ?     ?     ?  ?           1.000  
18  18     ?  24.650     ?     ?     ?     ?  ?           1.000  
19  19     ?  20.200     ?     ?     ?     ?  ?           1.000  
20  20     ?  22.780     ?     ?     ?     ?  ?           1.000  
21  21     ?  41.990     ?     ?     ?     ?  ?           1.000  
22  22     ?  22.280     ?     ?     ?     ?  ?           1.000  
23  23     ?  27.640     ?     ?     ?     ?  ?           1.000  
24  24     ?  24.980     ?     ?     ?     ?  ?           1.000  
25  25     ?  23.560     ?     ?     ?     ?  ?           1.000  
26  26     ?  28.610     ?     ?     ?     ?  ?           1.000  
27  27     ?  27.070     ?     ?     ?     ?  ?           1.000  
28  28     ?  44.210     ?     ?     ?     ?  ?           1.000  
29  29     ?  23.410     ?     ?     ?     ?  ?           1.000  
30  30     ?  20.450     ?     ?     ?     ?  ?           1.000  
31  31     ?  12.960     ?     ?     ?     ?  ?           1.000  
32  32     ?  26.050     ?     ?     ?     ?  ?           1.000  
33  33     ?  26.450     ?     ?     ?     ?  ?           1.000  
34  34     ?  22.570     ?     ?     ?     ?  ?           1.000  
35  35     ?  17.390     ?     ?     ?     ?  ?           1.000  
36  36     ?  37.950     ?     ?     ?     ?  ?           1.000  
37  37     ?  26.540     ?     ?     ?     ?  ?           1.000  
38  38     ?  18.060     ?     ?     ?     ?  ?           1.000  
39  39     ?  17.040     ?     ?     ?     ?  ?           1.000  
40  40     ?  28.180     ?     ?     ?     ?  ?           1.000  
41  41     ?  23.320     ?     ?     ?     ?  ?           1.000  
42  42     ?  30.570     ?     ?     ?     ?  ?           1.000  
43  43     ?  38.420     ?     ?     ?     ?  ?           1.000  
44  44     ?  20.060     ?     ?     ?     ?  ?           1.000  
45  45     ?  15.360     ?     ?     ?     ?  ?           1.000  
46  46     ?  29.820     ?     ?     ?     ?  ?           1.000  
47  47     ?  30.180     ?     ?     ?     ?  ?           1.000  
48  48     ?  21.630     ?     ?     ?     ?  ?           1.000  
49  49     ?  31.250     ?     ?     ?     ?  ?           1.000  
50  50     ?  28.070     ?     ?     ?     ?  ?           1.000  
51  51     ?  32.290     ?     ?     ?     ?  ?           1.000  
52  52     ?  41.350     ?     ?     ?     ?  ?           1.000  
53  53     ?  34.420     ?     ?     ?     ?  ?           1.000  
54  54     ?  28.160     ?     ?     ?     ?  ?           1.000  
55  55     ?  18.330     ?     ?     ?     ?  ?           1.000  
56  56     ?  34.170     ?     ?     ?     ?  ?           1.000  
57  57     ?  23.520     ?     ?     ?     ?  ?           1.000  
58  58     ?  34.010     ?     ?     ?     ?  ?           1.000  
59  59     ?  29.250     ?     ?     ?     ?  ?           1.000  
60  60     ?  27.790     ?     ?     ?     ?  ?           1.000  
61  61     ?  33.610     ?     ?     ?     ?  ?           1.000  
62  62     ?  36.060     ?     ?     ?     ?  ?           1.000  
63  63     ?  41.300     ?     ?     ?     ?  ?           1.000  
64  64     ?  40.410     ?     ?     ?     ?  ?           1.000  
65  65     ?  26.460     ?     ?     ?     ?  ?           1.000  
66  66     ?  22.800     ?     ?     ?     ?  ?           1.000  
67  67     ?  26.870     ?     ?     ?     ?  ?           1.000  
68  68     ?  36.350     ?     ?     ?     ?  ?           1.000  
69  69     ?  33.210     ?     ?     ?     ?  ?           1.000  
70  70     ?  34.850     ?     ?     ?     ?  ?           1.000  
71  71     ?  34.370     ?     ?     ?     ?  ?           1.000  
72  72     ?  41.430     ?     ?     ?     ?  ?           1.000  
73  73     ?  28.780     ?     ?     ?     ?  ?           1.000  
74  74     ?  47.810     ?     ?     ?     ?  ?           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  0.56  2.40  
2  4  C6     1  0.56  2.40  
#
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  0.957  0.059  -0.743  
 2   2  22  0.967  0.061  -0.704  
 3   3  20  0.978  0.052  -0.899  
 4   4  19  0.953  0.073  -0.518  
 5   5  22  0.977  0.052  -0.878  
 6   6  20  0.976  0.053  -0.884  
 7   7  19  0.954  0.079  -0.421  
 8   8  19  0.948  0.096  -0.146  
 9   9   1  0.991  0.034       ?  
10  10   1  0.936  0.106       ?  
11  11   1  0.922  0.093       ?  
12  12   1  0.835  0.457       ?  
13  13   1  0.920  0.113       ?  
14  14   1  0.978  0.175       ?  
15  15   1  0.992  0.068       ?  
16  16   1  0.915  0.136       ?  
17  17   1  0.942  0.095       ?  
18  18   1  0.935  0.118       ?  
19  19   1  0.948  0.097       ?  
20  20   1  0.874  0.075       ?  
21  21   1  0.644  0.246       ?  
22  22   1  0.926  0.079       ?  
23  23   1  0.876  0.114       ?  
24  24   1  0.877  0.112       ?  
25  25   1  0.948  0.081       ?  
26  26   1  0.881  0.098       ?  
27  27   1  0.939  0.087       ?  
28  28   1  0.636  0.164       ?  
29  29   1  0.951  0.072       ?  
30  30   1  0.900  0.085       ?  
31  31   1  0.993  0.052       ?  
32  32   1  0.881  0.133       ?  
33  33   1  0.944  0.149       ?  
34  34   1  0.906  0.124       ?  
35  35   1  0.971  0.066       ?  
36  36   1  0.663  0.187       ?  
37  37   1  0.936  0.114       ?  
38  38   1  0.979  0.090       ?  
39  39   1  0.993  0.026       ?  
40  40   1  0.952  0.111       ?  
41  41   1  0.811  0.097       ?  
42  42   1  0.885  0.156       ?  
43  43   1  0.789  0.150       ?  
44  44   1  0.960  0.046       ?  
45  45   1  0.979  0.059       ?  
46  46   1  0.924  0.067       ?  
47  47   1  0.623  0.300       ?  
48  48   1  0.905  0.098       ?  
49  49   1  0.846  0.204       ?  
50  50   1  0.888  0.213       ?  
51  51   1  0.801  0.155       ?  
52  52   1  0.829  0.143       ?  
53  53   1  0.806  0.374       ?  
54  54   1  0.937  0.072       ?  
55  55   1  0.955  0.049       ?  
56  56   1  0.806  0.162       ?  
57  57   1  0.920  0.132       ?  
58  58   1  0.765  0.210       ?  
59  59   1  0.706  0.296       ?  
60  60   1  0.945  0.118       ?  
61  61   1  0.788  0.178       ?  
62  62   1  0.817  0.125       ?  
63  63   1  0.683  0.211       ?  
64  64   1  0.905  0.452       ?  
65  65   1  0.904  0.192       ?  
66  66   1  0.937  0.134       ?  
67  67   1  0.937  0.333       ?  
68  68   1  0.791  0.332       ?  
69  69   1  0.893  0.294       ?  
70  70   1  0.862  0.127       ?  
71  71   1  0.764  0.170       ?  
72  72   1  0.873  0.620       ?  
73  73   1  0.711  0.463       ?  
74  74   1  0.655  0.183       ?  
#
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          2.36                                                                  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  
##
