data_8CS7

_entry.id  8CS7
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1  polymer  syn  "DNA (5'-D(*CP*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')"  6393.138  1  ?  ?  ?  ?  
2  polymer  syn  "DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')"                                           2082.400  1  ?  ?  ?  ?  
3  polymer  syn  "DNA (5'-D(P*GP*GP*CP*TP*G)-3')"                                                 1536.035  1  ?  ?  ?  ?  
4  polymer  syn  "DNA (5'-D(*CP*CP*GP*TP*GP*AP*TP*GP*T)-3')"                                      2746.809  1  ?  ?  ?  ?  
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A  ?     N  1  ?  
B  ?     N  2  ?  
C  ?     N  3  ?  
D  ?     N  4  ?  
#
_pdbx_vrpt_database.id             PDB
_pdbx_vrpt_database.code           8CS7
_pdbx_vrpt_database.extended_code  pdb_00008cs7
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    8CS7
_pdbx_vrpt_summary.extended_entry_id           pdb_00008cs7
_pdbx_vrpt_summary.PDB_deposition_date         2022-05-12
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2023-10-25
_pdbx_vrpt_summary.report_creation_date        2026-03-08:04:43
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,validation_schema,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*CP*GP*CP*AP*GP*CP*CP*TP*GP*TP*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')"  
2  polymer  "DNA (5'-D(P*CP*CP*GP*TP*AP*CP*A)-3')"  
3  polymer  "DNA (5'-D(P*GP*GP*CP*TP*G)-3')"  
4  polymer  "DNA (5'-D(*CP*CP*GP*TP*GP*AP*TP*GP*T)-3')"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  6.67  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  12.71  190562     ?     ?  
2  2  1  48.45    1001  4.04  9.32  
3  1  2   0.55  180081     ?     ?  
4  2  2   5.19    1155  4.00  9.00  
5  1  3   8.43  180053     ?     ?  
6  2  3  69.38    1162  4.00  9.00  
#
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   0.35  
2  4  2  A  1  1  A   3.46  
3  3  2  B  1  2  B   1.08  
4  4  2  B  1  2  B   7.36  
5  3  2  C  1  3  C   2.65  
6  4  2  C  1  3  C  10.30  
7  3  2  D  1  4  D   0.74  
8  4  2  D  1  4  D   6.06  
#
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  0.55  0.30  475  730  
2  1  2  B  B  0.36  0.19  157  239  
3  1  3  C  C  0.52  0.31  117  179  
4  1  4  D  D  0.54  0.26  203  312  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       15.06
_pdbx_vrpt_summary_geometry.num_H_reduce     476
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   952
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.27
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1460
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.52
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            0.000
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         331.814
_pdbx_vrpt_summary_diffraction.I_over_sigma              0.35(6.70A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        857
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.000
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.445
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.282
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.939
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.107
_pdbx_vrpt_summary_diffraction.DCC_R                     0.2289
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.2922
_pdbx_vrpt_summary_diffraction.EDS_R                     0.2577
_pdbx_vrpt_summary_diffraction.EDS_res_high              6.67
_pdbx_vrpt_summary_diffraction.EDS_res_low               39.41
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[329.195,329.195,344.388,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.045
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 8.41% 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         75.13
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      46
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.67
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     38.10
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       6.67
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        39.41
_pdbx_vrpt_summary_diffraction.PDB_R                     0.2305
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.2904
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.12
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.010 (Gargrove)"
#
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  DC  A  101  .  ?        ?  
 2  1  1  A   2  DC  A  102  .  ?        1  
 3  1  1  A   3  DG  A  103  .  ?        2  
 4  1  1  A   4  DC  A  104  .  ?        3  
 5  1  1  A   5  DA  A  105  .  ?        2  
 6  1  1  A   6  DG  A  106  .  ?        1  
 7  1  1  A   7  DC  A  107  .  ?        1  
 8  1  1  A   8  DC  A  108  .  ?        ?  
 9  1  1  A   9  DT  A  109  .  ?        ?  
10  1  1  A  10  DG  A  110  .  ?        ?  
11  1  1  A  11  DT  A  111  .  ?        1  
12  1  1  A  12  DA  A  112  .  ?        3  
13  1  1  A  13  DC  A  113  .  ?        1  
14  1  1  A  14  DG  A  114  .  ?        2  
15  1  1  A  15  DG  A  115  .  ?        1  
16  1  1  A  16  DA  A  116  .  ?        ?  
17  1  1  A  17  DC  A  117  .  ?        ?  
18  1  1  A  18  DA  A  118  .  ?        1  
19  1  1  A  19  DT  A  119  .  ?        1  
20  1  1  A  20  DC  A  120  .  ?        ?  
21  1  1  A  21  DA  A  121  .  ?        ?  
22  1  2  B   1  DC  B  119  .  ?        ?  
23  1  2  B   2  DC  B  120  .  ?        ?  
24  1  2  B   3  DG  B  121  .  ?        ?  
25  1  2  B   4  DT  B  122  .  ?        ?  
26  1  2  B   5  DA  B  123  .  ?        1  
27  1  2  B   6  DC  B  124  .  ?        2  
28  1  2  B   7  DA  B  125  .  ?        1  
29  1  3  C   1  DG  C  209  .  ?        ?  
30  1  3  C   2  DG  C  210  .  ?        ?  
31  1  3  C   3  DC  C  211  .  ?        ?  
32  1  3  C   4  DT  C  212  .  ?        2  
33  1  3  C   5  DG  C  213  .  ?        2  
34  1  4  D   1  DC  D  100  .  ?        1  
35  1  4  D   2  DC  D  101  .  ?        2  
36  1  4  D   3  DG  D  102  .  ?        2  
37  1  4  D   4  DT  D  103  .  ?        4  
38  1  4  D   5  DG  D  104  .  ?        1  
39  1  4  D   6  DA  D  105  .  ?        ?  
40  1  4  D   7  DT  D  106  .  ?        ?  
41  1  4  D   8  DG  D  107  .  ?        ?  
42  1  4  D   9  DT  D  108  .  ?        ?  
#
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  696.790  18  0.28  28  0.51  molprobity  1.000  
 2   2  11  648.770  21  0.45  32  0.66  molprobity  1.000  
 3   3  11  573.850  25  0.33  39  0.71  molprobity  1.000  
 4   4  11  610.850  21  0.18  32  0.30  molprobity  1.000  
 5   5  11  568.940  24  0.18  37  0.35  molprobity  1.000  
 6   6  11  605.610  25  0.38  39  0.59  molprobity  1.000  
 7   7  11  505.950  21  0.20  32  0.41  molprobity  1.000  
 8   8  11  473.760  21  0.12  32  0.29  molprobity  1.000  
 9   9  12  654.520  22  0.14  34  0.65  molprobity  1.000  
10  10  11  415.620  25  0.31  39  0.45  molprobity  1.000  
11  11  12  443.600  22  0.48  34  0.79  molprobity  1.000  
12  12  11  571.540  24  0.55  37  0.88  molprobity  1.000  
13  13  11  555.060  21  0.21  32  0.48  molprobity  1.000  
14  14  11  509.610  25  0.37  39  0.70  molprobity  1.000  
15  15  11  465.710  25  0.25  39  0.50  molprobity  1.000  
16  16  11  583.000  24  0.24  37  0.38  molprobity  1.000  
17  17  11  440.350  21  0.16  32  0.44  molprobity  1.000  
18  18  11  435.630  24  0.17  37  0.41  molprobity  1.000  
19  19  12  512.550  22  0.32  34  0.78  molprobity  1.000  
20  20  11  693.350  21  0.16  32  0.36  molprobity  1.000  
21  21  12  641.020  23  0.14  33  0.14  molprobity  1.000  
22  22  11  484.150  21  0.16  32  0.35  molprobity  1.000  
23  23  11  389.200  21  0.26  32  0.47  molprobity  1.000  
24  24  11  506.270  25  0.10  39  0.18  molprobity  1.000  
25  25  12  481.020  22  0.27  34  0.62  molprobity  1.000  
26  26  11  346.540  24  0.14  37  0.18  molprobity  1.000  
27  27  11  377.300  21  0.19  32  0.27  molprobity  1.000  
28  28  12  442.830  23  0.15  33  0.20  molprobity  1.000  
29  29  11  578.900  25  0.14  39  0.44  molprobity  1.000  
30  30  11  665.090  25  0.38  39  0.44  molprobity  1.000  
31  31  11  685.050  21  0.42  32  0.68  molprobity  1.000  
32  32  12  638.380  22  0.34  34  0.65  molprobity  1.000  
33  33  12  711.890  24  0.17  35  0.34  molprobity  1.000  
34  34  12  695.600  18  0.28  28  0.38  molprobity  1.000  
35  35  11  537.360  21  0.16  32  0.33  molprobity  1.000  
36  36  11  523.670  25  0.32  39  0.46  molprobity  1.000  
37  37  12  494.410  22  0.35  34  0.71  molprobity  1.000  
38  38  11  516.680  25  0.30  39  0.85  molprobity  1.000  
39  39  11  464.450  24  0.18  37  0.38  molprobity  1.000  
40  40  12  558.390  22  0.29  34  0.61  molprobity  1.000  
41  41  11  562.810  25  0.21  39  0.38  molprobity  1.000  
42  42  13  476.390  21  0.16  30  0.47  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   2  "H2''"   1  0.48  2.14  
 2   3  "H2''"   2  0.80  1.63  
 3   3  OP1      1  0.48  2.14  
 4   4  "H5''"   2  0.80  1.63  
 5   4  "H2''"   3  0.43  2.54  
 6   4  "H2''"   4  0.41  1.86  
 7   5  C8       3  0.43  2.54  
 8   5  H8       4  0.41  1.86  
 9   6  "H4'"    5  0.51  2.10  
10   7  OP1      5  0.51  2.10  
11  11  "H1'"    6  0.41  2.21  
12  12  OP1      7  0.43  2.02  
13  12  H8       7  0.43  2.02  
14  12  OP2      6  0.41  2.21  
15  13  "H2''"   8  0.46  2.30  
16  14  N7       8  0.46  2.30  
17  14  "H2''"   9  0.41  2.55  
18  15  C8       9  0.41  2.55  
19  18  "H2''"  10  0.58  1.84  
20  19  H72     10  0.58  1.84  
21  26  "H2''"  11  0.60  2.37  
22  27  C5      11  0.60  2.37  
23  27  N4      12  0.44  2.14  
24  28  H62     12  0.44  2.14  
25  32  "H2'"   13  0.52  2.45  
26  32  "H2''"  14  0.42  2.18  
27  33  C8      13  0.52  2.45  
28  33  OP1     14  0.42  2.18  
29  34  C2      15  0.44  3.06  
30  35  C2      16  0.50  2.99  
31  35  C5      15  0.44  3.06  
32  36  "H1'"   17  0.52  2.09  
33  36  C8      16  0.50  2.99  
34  37  "H2''"  18  0.56  2.40  
35  37  OP2     17  0.52  2.09  
36  37  "H2'"   19  0.42  2.20  
37  37  OP1     19  0.42  2.20  
38  38  C8      18  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
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
 1   1  16  0.945  0.174  1.228  0.096   0.000  
 2   2  19  0.959  0.257  2.470  0.207   0.000  
 3   3  22  0.937  0.219  2.069  0.147   0.000  
 4   4  19  0.930  0.288  2.934  0.343   5.260  
 5   5  21  0.892  0.199  1.893  0.132   0.000  
 6   6  22  0.904  0.185  1.534  0.146   0.000  
 7   7  19  0.952  0.151  0.883  0.220   0.000  
 8   8  19  0.875  0.114  0.329  0.087   0.000  
 9   9  20  0.967  0.282  2.773  0.098   0.000  
10  10  22  0.910  0.183  1.502  0.157   4.550  
11  11  20  0.975  0.373  4.131  0.080   0.000  
12  12  21  0.918  0.329  4.097  0.059   0.000  
13  13  19  0.968  0.327  3.518  0.058   5.260  
14  14  22  0.969  0.199  1.754  0.249   0.000  
15  15  22  0.926  0.140  0.825  0.270   4.550  
16  16  21  0.906  0.144  0.961  0.385   9.520  
17  17  19  0.828  0.151  0.883  0.379  10.530  
18  18  21  0.912  0.145  0.978  0.445   0.000  
19  19  20  0.925  0.448  5.251  0.099   0.000  
20  20  19  0.946  0.416  4.850  0.150   0.000  
21  21  21  0.940  0.293  3.486  0.040   0.000  
22  22  19  0.959  0.136  0.659  0.079   0.000  
23  23  19  0.957  0.107  0.225  0.076   5.260  
24  24  22  0.949  0.168  1.266  0.117   0.000  
25  25  20  0.721  0.212  1.728  0.163   0.000  
26  26  21  0.853  0.146  0.995  0.389   4.760  
27  27  19  0.894  0.363  4.057  0.117   0.000  
28  28  21  0.886  0.296  3.537  0.051   0.000  
29  29  22  0.781  0.197  1.723  0.173   0.000  
30  30  22  0.930  0.183  1.502  0.187   0.000  
31  31  19  0.946  0.153  0.913  0.144  10.530  
32  32  20  0.947  0.167  1.057  0.082   0.000  
33  33  22  0.875  0.239  2.384  0.079   0.000  
34  34  16  0.931  0.185  1.392  0.080   0.000  
35  35  19  0.919  0.167  1.123  0.205   0.000  
36  36  22  0.899  0.155  1.061  0.080   0.000  
37  37  20  0.910  0.130  0.504  0.086   0.000  
38  38  22  0.824  0.118  0.479  0.333   9.090  
39  39  21  0.646  0.157  1.181  0.465   4.760  
40  40  20  0.829  0.349  3.773  0.149   0.000  
41  41  22  0.889  0.440  5.550  0.143   0.000  
42  42  20  0.869  0.401  4.549  0.032   0.000  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity           "4-5-2 with Phenix2.0"                                              Y  
2  eds                  3.0                                                                 Y  
3  dcc                  '"2.31  (2025-03-10))"'                                             Y  
4  xtriage              2.0                                                                 Y  
5  percentiles          "20250101.v01 (using entries in the PDB archive January 1st 2025)"  Y  
6  validation-pipeline  2.49                                                                Y  
##
