data_6WT1

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6WT1
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6WT1
_pdbx_vrpt_summary.PDB_deposition_date         2020-05-01
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-18
_pdbx_vrpt_summary.report_creation_date        2023-10-09:07:54
_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*AP*AP*GP*AP*CP*TP*GP*CP*AP*CP*TP*CP*A)-3')"  
2  polymer      "DNA (5'-D(P*AP*GP*TP*CP*T)-3')"  
3  polymer      "DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*C)-3')"  
4  polymer      "DNA (5'-D(P*TP*GP*TP*CP*TP*GP*C)-3')"  
5  non-polymer  "MAGNESIUM 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  3.11  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   28.55  141614     ?     ?  
2  2  1   60.33    1389  3.10  3.14  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1260  3.10  3.14  
5  1  3   27.11  130704     ?     ?  
6  2  3   67.35    1292  3.10  3.14  
#
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  0.58  483  743  
2  1  2  B  B  1.49  0.86  113  172  
3  1  3  C  C  1.06  0.62  203  312  
4  1  4  D  D  1.09  0.59  157  240  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       9.74
_pdbx_vrpt_summary_geometry.num_H_reduce     478
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.63
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1467
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.02
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 10.000
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            68.307
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         98.559
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.71(3.11A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        4558
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.043
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.112
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.463
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.289
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.972
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.073;h,-h-k,-l:0.117;-k,-h,-l:0.089
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.22
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.11
_pdbx_vrpt_summary_diffraction.EDS_res_low               26.47
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[95.930,95.930,140.986,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.406
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 9.66% 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         83.22
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      242
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.31
_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        50.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.26
#
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.count_symm_clashes
 1  1  1  A   1  DG  A    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  .  ?        ?     ?     ?  
 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  DA  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  1  A  13  DC  A   13  .  ?        ?     ?     ?  
14  1  1  A  14  DT  A   14  .  ?        ?     1     ?  
15  1  1  A  15  DG  A   15  .  ?        ?     1     ?  
16  1  1  A  16  DC  A   16  .  ?        ?     ?     ?  
17  1  1  A  17  DA  A   17  .  ?        ?     1     ?  
18  1  1  A  18  DC  A   18  .  ?        ?     3     ?  
19  1  1  A  19  DT  A   19  .  ?        ?     2     ?  
20  1  1  A  20  DC  A   20  .  ?        ?     ?     ?  
21  1  1  A  21  DA  A   21  .  ?        ?     ?     ?  
22  1  2  B   1  DA  B    1  .  ?        1     ?     ?  
23  1  2  B   2  DG  B    2  .  ?        ?     ?     ?  
24  1  2  B   3  DT  B    3  .  ?        ?     2     ?  
25  1  2  B   4  DC  B    4  .  ?        ?     2     ?  
26  1  2  B   5  DT  B    5  .  ?        2     ?     ?  
27  1  3  C   1  DT  C    1  .  ?        ?     ?     ?  
28  1  3  C   2  DC  C    2  .  ?        ?     ?     ?  
29  1  3  C   3  DT  C    3  .  ?        ?     ?     ?  
30  1  3  C   4  DG  C    4  .  ?        ?     ?     ?  
31  1  3  C   5  DA  C    5  .  ?        ?     ?     ?  
32  1  3  C   6  DG  C    6  .  ?        ?     ?     ?  
33  1  3  C   7  DT  C    7  .  ?        ?     2     ?  
34  1  3  C   8  DG  C    8  .  ?        ?     4     ?  
35  1  3  C   9  DC  C    9  .  ?        1     2     1  
36  1  4  D   1  DT  D   10  .  ?        ?     ?     1  
37  1  4  D   2  DG  D   11  .  ?        1     ?     ?  
38  1  4  D   3  DT  D   12  .  ?        ?     2     ?  
39  1  4  D   4  DC  D   13  .  ?        ?     2     ?  
40  1  4  D   5  DT  D   14  .  ?        ?     ?     ?  
41  1  4  D   6  DG  D   15  .  ?        ?     1     ?  
42  1  4  D   7  DC  D   16  .  ?        ?     1     ?  
43  1  5  E   .  MG  B  101  .  ?        ?     ?     ?  
44  1  5  F   .  MG  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  201.170    22  0.28    35  0.51  molprobity  1.000  
 2   2    11  200.440    24  0.46    37  0.82  molprobity  1.000  
 3   3    11  174.750    25  0.47    39  0.75  molprobity  1.000  
 4   4    11  187.760    21  0.52    32  0.95  molprobity  1.000  
 5   5    11  168.030    24  0.28    37  0.80  molprobity  1.000  
 6   6    11  166.320    25  0.49    39  0.64  molprobity  1.000  
 7   7    11  140.540    24  0.58    37  0.62  molprobity  1.000  
 8   8    11  147.730    21  0.40    32  1.02  molprobity  1.000  
 9   9    11  131.960    24  0.45    37  0.64  molprobity  1.000  
10  10    11  128.690    24  0.47    37  0.65  molprobity  1.000  
11  11    11  115.240    25  0.37    39  0.78  molprobity  1.000  
12  12    11  132.320    24  0.50    37  0.65  molprobity  1.000  
13  13    11  122.590    21  0.65    32  0.81  molprobity  1.000  
14  14    12  104.890    22  0.39    34  0.58  molprobity  1.000  
15  15    11   81.580    25  0.94    39  0.81  molprobity  1.000  
16  16    11  100.350    21  1.14    32  1.07  molprobity  1.000  
17  17    11   96.290    24  0.60    37  1.01  molprobity  1.000  
18  18    11  103.470    21  0.87    32  0.97  molprobity  1.000  
19  19    12  103.930    22  0.68    34  1.10  molprobity  1.000  
20  20    11  150.740    21  0.69    32  1.05  molprobity  1.000  
21  21    12  189.250    23  0.29    33  0.62  molprobity  1.000  
22  22    11   75.520    24  0.83    37  1.42  molprobity  1.000  
23  23    11   79.010    25  0.91    39  1.42  molprobity  1.000  
24  24    12   99.100    22  0.86    34  0.98  molprobity  1.000  
25  25    11   91.750    21  0.78    32  1.15  molprobity  1.000  
26  26    13   76.940    21  0.92    30  2.26  molprobity  1.000  
27  27    13  191.930    19  0.39    30  0.76  molprobity  1.000  
28  28    11  187.290    21  0.28    32  0.70  molprobity  1.000  
29  29    12  192.650    22  0.39    34  0.95  molprobity  1.000  
30  30    11  186.300    25  0.58    39  0.69  molprobity  1.000  
31  31    11  169.300    24  0.57    37  0.66  molprobity  1.000  
32  32    11  129.910    25  0.86    39  0.91  molprobity  1.000  
33  33    12   98.140    22  0.72    34  1.61  molprobity  1.000  
34  34    11   71.430    25  0.78    39  1.03  molprobity  1.000  
35  35    12   82.060    20  0.70    28  1.78  molprobity  1.000  
36  36    12   92.640    22  1.01    34  1.01  molprobity  1.000  
37  37    11   95.400    25  0.61    39  1.28  molprobity  1.000  
38  38    12  116.450    22  0.61    34  1.38  molprobity  1.000  
39  39    11  141.320    21  0.54    32  0.89  molprobity  1.000  
40  40    12  167.860    22  0.48    34  1.36  molprobity  1.000  
41  41    11  173.000    25  0.39    39  0.87  molprobity  1.000  
42  42    12  182.140    20  0.19    28  0.45  molprobity  1.000  
43  43     ?   74.190     ?     ?     ?     ?  ?           1.000  
44  44     ?   68.770     ?     ?     ?     ?  ?           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  14  "H1'"    1  0.45  1.99  
 2  15  "H5'"    1  0.45  1.99  
 3  17  C4       2  0.45  3.04  
 4  18  "H2''"   3  0.63  1.81  
 5  18  "H2'"    4  0.52  1.91  
 6  18  C5       2  0.45  3.04  
 7  19  "H5''"   3  0.63  1.81  
 8  19  H72      4  0.52  1.91  
 9  24  "H2''"   5  0.54  1.90  
10  24  "H2''"   6  0.50  2.41  
11  25  "H5''"   5  0.54  1.90  
12  25  "C5'"    6  0.50  2.41  
13  33  "H2''"   7  0.74  2.22  
14  33  "H2''"   8  0.42  1.81  
15  34  C8       7  0.74  2.22  
16  34  H8       8  0.42  1.81  
17  34  "H1'"    9  0.41  2.02  
18  34  "H1'"   10  0.40  2.20  
19  35  "H5'"    9  0.41  2.02  
20  35  "O4'"   10  0.40  2.20  
21  38  "H2''"  11  0.54  1.90  
22  38  "H2''"  12  0.42  2.49  
23  39  "H5''"  11  0.54  1.90  
24  39  "C5'"   12  0.42  2.49  
25  41  C4      13  0.42  3.07  
26  42  C5      13  0.42  3.07  
#
loop_
_pdbx_vrpt_instance_symm_clashes.ordinal
_pdbx_vrpt_instance_symm_clashes.instance_id
_pdbx_vrpt_instance_symm_clashes.label_atom_id
_pdbx_vrpt_instance_symm_clashes.scid
_pdbx_vrpt_instance_symm_clashes.symop
_pdbx_vrpt_instance_symm_clashes.clashmag
_pdbx_vrpt_instance_symm_clashes.dist
1  35  "O3'"  0  1_555  0.82  1.38  
2  36  OP2    0  2_554  0.82  1.38  
#
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  22  "O5'"  P      OP1     99.736  105.700  0.900  -6.63  
2  26  "C1'"  "O4'"  "C4'"  103.356  110.100  1.000  -6.74  
3  26  "O5'"  P      OP2    117.265  110.700  1.200   5.47  
4  35  "C1'"  "O4'"  "C4'"  104.174  110.100  1.000  -5.93  
5  37  "O5'"  P      OP2    100.956  105.700  0.900  -5.27  
#
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  0.950  0.062  -1.637  
 2   2  21  0.927  0.080  -1.440  
 3   3  22  0.908  0.095  -1.228  
 4   4  19  0.949  0.086  -1.351  
 5   5  21  0.926  0.103  -1.150  
 6   6  22  0.923  0.095  -1.228  
 7   7  21  0.922  0.090  -1.314  
 8   8  19  0.935  0.082  -1.397  
 9   9  21  0.944  0.091  -1.301  
10  10  21  0.964  0.083  -1.402  
11  11  22  0.959  0.075  -1.476  
12  12  21  0.960  0.083  -1.402  
13  13  19  0.957  0.088  -1.328  
14  14  20  0.973  0.098  -1.259  
15  15  22  0.973  0.067  -1.575  
16  16  19  0.963  0.092  -1.282  
17  17  21  0.955  0.072  -1.540  
18  18  19  0.946  0.083  -1.386  
19  19  20  0.915  0.139  -0.789  
20  20  19  0.924  0.095  -1.247  
21  21  21  0.967  0.068  -1.591  
22  22  21  0.971  0.079  -1.452  
23  23  22  0.974  0.063  -1.625  
24  24  20  0.969  0.092  -1.327  
25  25  19  0.964  0.103  -1.154  
26  26  20  0.962  0.131  -0.881  
27  27  17  0.936  0.100  -1.236  
28  28  19  0.933  0.067  -1.571  
29  29  20  0.944  0.074  -1.533  
30  30  22  0.939  0.076  -1.463  
31  31  21  0.928  0.087  -1.351  
32  32  22  0.920  0.087  -1.327  
33  33  20  0.947  0.102  -1.213  
34  34  22  0.956  0.099  -1.178  
35  35  19  0.968  0.095  -1.247  
36  36  20  0.968  0.104  -1.190  
37  37  22  0.960  0.085  -1.352  
38  38  20  0.950  0.081  -1.453  
39  39  19  0.925  0.090  -1.305  
40  40  20  0.944  0.092  -1.327  
41  41  22  0.941  0.060  -1.662  
42  42  19  0.946  0.065  -1.594  
43  43   1  0.962  0.279       ?  
44  44   1  0.959  0.102       ?  
#
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  
##
