data_7JFV

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7JFV
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7JFV
_pdbx_vrpt_summary.PDB_deposition_date         2020-07-17
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-10-18
_pdbx_vrpt_summary.report_creation_date        2023-10-11:00:57
_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(*GP*AP*GP*CP*AP*GP*AP*CP*CP*AP*GP*A)-3')"  
2  polymer  "DNA (5'-D(P*CP*GP*GP*TP*AP*CP*TP*CP*A)-3')"  
3  polymer  "DNA (5'-D(P*TP*CP*TP*CP*CP*G)-3')"  
4  polymer  "DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*AP*GP*GP*TP*CP*TP*GP*C)-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  3.1  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   60.84  141614     ?     ?  
2  2  1   86.23    1184  3.10  3.10  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1067  3.10  3.10  
5  1  3   57.97  130704     ?     ?  
6  2  3   91.64    1094  3.10  3.10  
#
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  0.79  0.62  279  429  
2  1  2  B  B  0.97  0.66  204  312  
3  1  3  C  C  1.11  0.73  131  199  
4  1  4  D  D  1.00  0.56  342  527  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       4.50
_pdbx_vrpt_summary_geometry.num_H_reduce     477
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   956
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.62
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1467
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.96
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            -10.000
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         63.267
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.37(3.12A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3707
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.026
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.466
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.294
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.981
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.055;h,-h-k,-l:0.090;-k,-h,-l:0.090
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.23
_pdbx_vrpt_summary_diffraction.EDS_R                     0.21
_pdbx_vrpt_summary_diffraction.EDS_res_high              3.10
_pdbx_vrpt_summary_diffraction.EDS_res_low               34.01
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[66.870,66.870,279.650,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           1.544
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 7.63% 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         8
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         73.27
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      362
_pdbx_vrpt_summary_diffraction.percent_free_reflections  9.77
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       3.10
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        34.01
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
_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_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  DC  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  2  B   1  DC  B  12  .  ?        ?  
14  1  2  B   2  DG  B  13  .  ?        1  
15  1  2  B   3  DG  B  14  .  ?        1  
16  1  2  B   4  DT  B  15  .  ?        ?  
17  1  2  B   5  DA  B  16  .  ?        1  
18  1  2  B   6  DC  B  17  .  ?        2  
19  1  2  B   7  DT  B  18  .  ?        1  
20  1  2  B   8  DC  B  19  .  ?        ?  
21  1  2  B   9  DA  B  20  .  ?        1  
22  1  3  C   1  DT  C   0  .  ?        ?  
23  1  3  C   2  DC  C   1  .  ?        ?  
24  1  3  C   3  DT  C   2  .  ?        ?  
25  1  3  C   4  DC  C   3  .  ?        ?  
26  1  3  C   5  DC  C   4  .  ?        ?  
27  1  3  C   6  DG  C   5  .  ?        ?  
28  1  4  D   1  DT  D   2  .  ?        ?  
29  1  4  D   2  DC  D   3  .  ?        ?  
30  1  4  D   3  DT  D   4  .  ?        1  
31  1  4  D   4  DG  D   5  .  ?        ?  
32  1  4  D   5  DA  D   6  .  ?        ?  
33  1  4  D   6  DG  D   7  .  ?        1  
34  1  4  D   7  DT  D   8  .  ?        1  
35  1  4  D   8  DA  D   9  .  ?        ?  
36  1  4  D   9  DG  D  10  .  ?        ?  
37  1  4  D  10  DG  D  11  .  ?        ?  
38  1  4  D  11  DT  D  12  .  ?        ?  
39  1  4  D  12  DC  D  13  .  ?        ?  
40  1  4  D  13  DT  D  14  .  ?        ?  
41  1  4  D  14  DG  D  15  .  ?        ?  
42  1  4  D  15  DC  D  16  .  ?        ?  
#
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  101.460  22  0.74  35  0.75  molprobity  1.000  
 2   2  11  125.430  24  0.45  37  0.64  molprobity  1.000  
 3   3  11  113.780  25  0.48  39  0.86  molprobity  1.000  
 4   4  11  110.640  21  0.70  32  0.86  molprobity  1.000  
 5   5  11  109.080  24  0.57  37  0.75  molprobity  1.000  
 6   6  11  111.180  25  0.57  39  0.73  molprobity  1.000  
 7   7  11  115.990  24  0.59  37  0.88  molprobity  1.000  
 8   8  11  113.420  21  0.63  32  0.99  molprobity  1.000  
 9   9  11  103.680  21  0.70  32  0.83  molprobity  1.000  
10  10  11   87.820  24  0.63  37  0.61  molprobity  1.000  
11  11  11   74.800  25  0.68  39  0.88  molprobity  1.000  
12  12  12   75.280  23  0.65  33  0.66  molprobity  1.000  
13  13  11   79.600  21  0.63  32  0.89  molprobity  1.000  
14  14  11   80.670  25  0.77  39  1.19  molprobity  1.000  
15  15  11   78.190  25  0.65  39  0.90  molprobity  1.000  
16  16  12   82.680  22  0.74  34  1.24  molprobity  1.000  
17  17  11   80.000  24  0.55  37  0.71  molprobity  1.000  
18  18  11   76.750  21  0.79  32  0.85  molprobity  1.000  
19  19  12   71.850  22  0.43  34  1.24  molprobity  1.000  
20  20  11   78.390  21  0.58  32  0.82  molprobity  1.000  
21  21  12   86.250  23  0.70  33  0.67  molprobity  1.000  
22  22  12   66.160  22  0.47  34  1.21  molprobity  1.000  
23  23  11   64.880  21  0.68  32  0.88  molprobity  1.000  
24  24  12   63.070  22  0.90  34  1.58  molprobity  1.000  
25  25  11   64.460  21  0.87  32  1.10  molprobity  1.000  
26  26  11   64.470  21  0.76  32  0.74  molprobity  1.000  
27  27  12   60.010  24  0.61  35  0.94  molprobity  1.000  
28  28  13  123.560  19  0.56  30  1.37  molprobity  1.000  
29  29  11  112.840  21  0.68  32  0.76  molprobity  1.000  
30  30  12  105.680  22  0.60  34  1.41  molprobity  1.000  
31  31  11   90.160  25  0.41  39  0.74  molprobity  1.000  
32  32  11   87.450  24  0.55  37  0.62  molprobity  1.000  
33  33  11   71.760  25  0.64  39  1.04  molprobity  1.000  
34  34  12   68.260  22  0.87  34  1.26  molprobity  1.000  
35  35  11   62.420  24  0.42  37  0.71  molprobity  1.000  
36  36  11   66.240  25  0.34  39  0.64  molprobity  1.000  
37  37  11   81.220  25  0.32  39  0.66  molprobity  1.000  
38  38  12  100.920  22  0.59  34  1.41  molprobity  1.000  
39  39  11  118.350  21  0.45  32  0.85  molprobity  1.000  
40  40  12  139.470  22  0.60  34  1.22  molprobity  1.000  
41  41  11  139.670  25  0.54  39  1.11  molprobity  1.000  
42  42  12  145.460  20  0.57  28  0.74  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  14  "H2''"  1  0.42  2.20  
 2  15  OP2     1  0.42  2.20  
 3  17  "H2''"  2  0.47  2.14  
 4  18  OP2     2  0.47  2.14  
 5  18  "H2''"  3  0.43  2.18  
 6  19  "O5'"   3  0.43  2.18  
 7  21  C2      4  0.47  2.49  
 8  30  H73     4  0.47  2.49  
 9  33  "H2''"  5  0.44  2.00  
10  34  "H5''"  5  0.44  2.00  
#
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  0.945  0.091  -1.278  
 2   2  21  0.932  0.083  -1.402  
 3   3  22  0.945  0.065  -1.600  
 4   4  19  0.963  0.067  -1.571  
 5   5  21  0.928  0.080  -1.440  
 6   6  22  0.967  0.059  -1.674  
 7   7  21  0.922  0.066  -1.616  
 8   8  19  0.956  0.061  -1.641  
 9   9  19  0.943  0.064  -1.606  
10  10  21  0.944  0.092  -1.288  
11  11  22  0.946  0.079  -1.426  
12  12  21  0.953  0.074  -1.515  
13  13  19  0.926  0.090  -1.305  
14  14  22  0.925  0.079  -1.426  
15  15  22  0.922  0.068  -1.563  
16  16  20  0.967  0.049  -1.819  
17  17  21  0.951  0.069  -1.578  
18  18  19  0.948  0.067  -1.571  
19  19  20  0.956  0.078  -1.487  
20  20  19  0.955  0.089  -1.316  
21  21  21  0.908  0.145  -0.621  
22  22  20  0.939  0.097  -1.270  
23  23  19  0.933  0.084  -1.374  
24  24  20  0.936  0.127  -0.927  
25  25  19  0.958  0.086  -1.351  
26  26  19  0.983  0.039  -1.896  
27  27  22  0.936  0.078  -1.439  
28  28  17  0.965  0.068  -1.602  
29  29  19  0.915  0.072  -1.513  
30  30  20  0.922  0.072  -1.556  
31  31  22  0.945  0.069  -1.550  
32  32  21  0.943  0.065  -1.628  
33  33  22  0.962  0.059  -1.674  
34  34  20  0.960  0.082  -1.442  
35  35  21  0.959  0.097  -1.225  
36  36  22  0.963  0.070  -1.538  
37  37  22  0.966  0.071  -1.525  
38  38  20  0.945  0.072  -1.556  
39  39  19  0.936  0.053  -1.733  
40  40  20  0.929  0.059  -1.705  
41  41  22  0.938  0.055  -1.724  
42  42  19  0.953  0.062  -1.629  
#
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          2.35.1                                                                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  
##
