data_8EPB

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  8EPB
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8EPB
_pdbx_vrpt_summary.PDB_deposition_date         2022-10-05
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2024-04-03
_pdbx_vrpt_summary.report_creation_date        2024-03-28:12:41
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,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(*CP*GP*CP*TP*GP*GP*TP*GP*GP*TP*TP*CP*GP*A)-3')"  
2  polymer  "DNA (5'-D(*GP*AP*CP*CP*AP*GP*CP*CP*GP*AP*AP*CP*CP*T)-3')"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  2.61  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   17.65  141614     ?     ?  
2  2  1   32.17    4168  2.60  2.64  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    3731  2.60  2.64  
5  1  3    8.24  130704     ?     ?  
6  2  3   14.54    3797  2.60  2.64  
#
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  
#
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  1.52  1.32  321  495  
2  1  2  B  B  1.25  1.20  315  483  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       13.56
_pdbx_vrpt_summary_geometry.num_H_reduce     317
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   636
_pdbx_vrpt_summary_geometry.bonds_RMSZ       1.26
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  978
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.39
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 424.724
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            -9.446
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         56.068
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.58(2.61A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1876
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.674
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.185
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.456
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.288
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.926
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.187;h,-h-k,-l:0.257;-k,-h,-l:0.248
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.29
_pdbx_vrpt_summary_diffraction.EDS_R                     0.21
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.61
_pdbx_vrpt_summary_diffraction.EDS_res_low               32.88
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[64.936,64.936,54.969,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.162
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 27.76 % of the origin peak, indicating pseudo-translational symmetry.  The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 2.0781e-03. The detected translational NCS is most likely also responsible for the elevated intensity ratio.  See the relevant section of the logfile for more details."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         3
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         54.90
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      86
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.58
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.61
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        29.73
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.29
#
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  DC  A   1  .  ?        ?     ?     1  
 2  1  1  A   2  DG  A   2  .  ?        ?     ?     1  
 3  1  1  A   3  DC  A   3  .  ?        ?     ?     1  
 4  1  1  A   4  DT  A   4  .  ?        ?     ?     ?  
 5  1  1  A   5  DG  A   5  .  ?        1     3     1  
 6  1  1  A   6  DG  A   6  .  ?        ?     ?     2  
 7  1  1  A   7  DT  A   7  .  ?        ?     1     1  
 8  1  1  A   8  DG  A   8  .  ?        ?     1     1  
 9  1  1  A   9  DG  A   9  .  ?        ?     1     1  
10  1  1  A  10  DT  A  10  .  ?        1     ?     1  
11  1  1  A  11  DT  A  11  .  ?        ?     ?     ?  
12  1  1  A  12  DC  A  12  .  ?        1     ?     1  
13  1  1  A  13  DG  A  13  .  ?        ?     ?     1  
14  1  1  A  14  DA  A  14  .  ?        ?     ?     ?  
15  1  2  B   1  DG  B   1  .  ?        ?     ?     2  
16  1  2  B   2  DA  B   2  .  ?        1     ?     ?  
17  1  2  B   3  DC  B   3  .  ?        ?     ?     1  
18  1  2  B   4  DC  B   4  .  ?        1     ?     1  
19  1  2  B   5  DA  B   5  .  ?        ?     ?     ?  
20  1  2  B   6  DG  B   6  .  ?        ?     ?     1  
21  1  2  B   7  DC  B   7  .  ?        ?     ?     2  
22  1  2  B   8  DC  B   8  .  ?        ?     ?     1  
23  1  2  B   9  DG  B   9  .  ?        ?     ?     1  
24  1  2  B  10  DA  B  10  .  ?        ?     ?     ?  
25  1  2  B  11  DA  B  11  .  ?        ?     ?     ?  
26  1  2  B  12  DC  B  12  .  ?        ?     ?     ?  
27  1  2  B  13  DC  B  13  .  ?        ?     ?     1  
28  1  2  B  14  DT  B  14  .  ?        ?     ?     ?  
#
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  39.460  18  0.90  28  1.21  molprobity  1.000  
 2   2  11  41.270  25  0.83  39  0.90  molprobity  1.000  
 3   3  11  42.100  21  1.30  32  1.31  molprobity  1.000  
 4   4  12  41.810  22  1.19  34  1.84  molprobity  1.000  
 5   5  11  40.190  25  1.61  39  2.28  molprobity  1.000  
 6   6  11  40.160  25  1.18  39  1.07  molprobity  1.000  
 7   7  12  39.040  22  0.74  34  1.53  molprobity  1.000  
 8   8  11  37.980  25  1.73  39  1.70  molprobity  1.000  
 9   9  11  36.450  25  1.41  39  1.86  molprobity  1.000  
10  10  12  35.150  22  1.91  34  1.95  molprobity  1.000  
11  11  12  37.890  22  0.92  34  1.68  molprobity  1.000  
12  12  11  38.590  21  1.61  32  0.95  molprobity  1.000  
13  13  11  43.940  25  1.37  39  1.17  molprobity  1.000  
14  14  12  45.520  23  1.07  33  0.68  molprobity  1.000  
15  15  12  45.420  22  1.17  35  1.05  molprobity  1.000  
16  16  11  47.420  24  1.48  37  1.22  molprobity  1.000  
17  17  11  46.380  21  1.05  32  1.38  molprobity  1.000  
18  18  11  44.240  21  1.47  32  1.16  molprobity  1.000  
19  19  11  46.600  24  1.26  37  1.21  molprobity  1.000  
20  20  11  55.040  25  1.17  39  1.17  molprobity  1.000  
21  21  11  56.780  21  1.38  32  1.38  molprobity  1.000  
22  22  11  49.780  21  1.20  32  1.02  molprobity  1.000  
23  23  11  41.660  25  1.15  39  1.31  molprobity  1.000  
24  24  11  37.330  24  0.96  37  1.20  molprobity  1.000  
25  25  11  37.390  24  1.28  37  1.10  molprobity  1.000  
26  26  11  39.810  21  1.02  32  1.35  molprobity  1.000  
27  27  11  39.320  21  1.03  32  1.62  molprobity  1.000  
28  28  13  46.280  21  1.05  30  1.27  molprobity  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  "H2''"   1  0.41  2.02  
 2   2  "H5'"    1  0.41  2.02  
 3   3  H42      2  0.49  1.59  
 4   5  "H1'"    3  0.60  2.36  
 5   6  "H1'"    4  0.62  1.82  
 6   6  C8       3  0.60  2.36  
 7   7  "H5'"    4  0.62  1.82  
 8   8  O6       5  0.85  2.09  
 9   9  "H2''"   6  0.56  1.87  
10  10  H71      6  0.56  1.87  
11  12  "H2''"   7  0.62  2.33  
12  13  C8       7  0.62  2.33  
13  15  "H5'"    8  0.40  1.86  
14  15  H8       8  0.40  1.86  
15  17  "H2''"   9  0.48  2.13  
16  18  OP2      9  0.48  2.13  
17  20  H1       2  0.49  1.59  
18  21  OP2     10  0.43  2.18  
19  21  "H2'"   10  0.43  2.18  
20  22  "H2''"  11  0.41  2.55  
21  23  C8      11  0.41  2.55  
22  27  N4       5  0.85  2.09  
#
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   5  N9     C4     1.334  1.375  0.008  -5.13  
2  10  "C3'"  "O3'"  1.511  1.435  0.013   5.84  
3  12  "C3'"  "O3'"  1.362  1.435  0.013  -5.58  
4  16  "C3'"  "O3'"  1.364  1.435  0.013  -5.47  
5  18  "C3'"  "O3'"  1.363  1.435  0.013  -5.51  
#
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
_pdbx_vrpt_instance_intra_angle_outliers.link
1  5  "C3'"  "C2'"  "C1'"   95.885  102.500  1.200  -5.51  ?     
2  5  "C4'"  "C3'"  "C2'"   98.003  103.100  0.900  -5.66  ?     
3  5  "O4'"  "C4'"  "C3'"  101.347  106.000  0.600  -7.75  ?     
4  7  N3     C4     O4     122.933  119.900  0.600   5.05  ?     
5  8  OP2    P      "O3'"  116.254  105.200  2.200   5.03  Y     
6  9  "O4'"  "C1'"  N9     111.731  108.000  0.700   5.33  ?     
#
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  0.962  0.113  -1.036  
 2   2  22  0.959  0.105  -1.146  
 3   3  19  0.952  0.104  -1.172  
 4   4  20  0.950  0.115  -0.950  
 5   5  22  0.966  0.097  -1.281  
 6   6  22  0.916  0.130  -0.726  
 7   7  20  0.938  0.107  -1.065  
 8   8  22  0.947  0.112  -1.029  
 9   9  22  0.966  0.096  -1.297  
10  10  20  0.964  0.115  -0.950  
11  11  20  0.960  0.098  -1.194  
12  12  19  0.969  0.094  -1.323  
13  13  22  0.959  0.106  -1.129  
14  14  21  0.951  0.112  -0.986  
15  15  19  0.928  0.133  -0.676  
16  16  21  0.905  0.127  -0.755  
17  17  19  0.930  0.124  -0.870  
18  18  19  0.961  0.106  -1.142  
19  19  21  0.936  0.107  -1.063  
20  20  22  0.899  0.120  -0.894  
21  21  19  0.913  0.133  -0.734  
22  22  19  0.955  0.120  -0.931  
23  23  22  0.960  0.120  -0.894  
24  24  21  0.962  0.099  -1.186  
25  25  21  0.962  0.095  -1.248  
26  26  19  0.912  0.158  -0.356  
27  27  19  0.947  0.135  -0.704  
28  28  20  0.933  0.156  -0.361  
#
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  eds          2.36.1                                                                Y  
3  dcc          '"2.27  (2023-04-10)"'                                                Y  
4  xtriage      1.13                                                                  Y  
5  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
