data_7BPV

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7BPV
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7BPV
_pdbx_vrpt_summary.PDB_deposition_date         2020-03-23
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2023-11-29
_pdbx_vrpt_summary.RNA_suiteness               0.62
_pdbx_vrpt_summary.report_creation_date        2023-11-19:11:07
_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      "RNA (5'-R(P*GP*UP*GP*GP*GP*CP*CP*GP*AP*C)-3')"  
2  polymer      "DNA (5'-D(P*GP*TP*CP*GP*GP*CP*CP*CP*AP*C)-3')"  
3  non-polymer  "SULFATE ION"  
4  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  4  
E  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  1.781  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         
4  RNAsuiteness_percent   
#
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   92.45  141614     ?     ?  
2  2  1   90.97   10184  1.76  1.80  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    9032  1.76  1.80  
5  1  3   46.99  130704     ?     ?  
6  2  3   23.54    9185  1.76  1.80  
7  1  4   69.83    3102     ?     ?  
8  2  4   50.61    1069  1.16  2.40  
#
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  S  100.00  
2  4  2  A  1  1  S  100.00  
3  3  2  B  1  2  A  100.00  
4  4  2  B  1  2  A  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  S  0.96  0.85  243  376  
2  1  2  B  A  0.93  1.06  226  344  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       1.54
_pdbx_vrpt_summary_geometry.num_H_reduce     222
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   469
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.96
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  720
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.95
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 103.387
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            47.296
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         38.426
_pdbx_vrpt_summary_diffraction.I_over_sigma              3.26(1.78A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        6361
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.266
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.385
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.477
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.309
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.958
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,l,k:0.045
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.23
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.78
_pdbx_vrpt_summary_diffraction.EDS_res_low               21.61
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[48.112,35.106,35.309,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.329
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 10.08% 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         98.68
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      642
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.09
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.78
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        21.61
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.24
#
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_clashes
 1  1  1  A   1  G    S    1  .  ?        1     ?  
 2  1  1  A   2  U    S    2  .  ?        ?     ?  
 3  1  1  A   3  G    S    3  .  ?        ?     ?  
 4  1  1  A   4  G    S    4  .  ?        ?     ?  
 5  1  1  A   5  G    S    5  .  ?        ?     ?  
 6  1  1  A   6  C    S    6  .  ?        ?     ?  
 7  1  1  A   7  C    S    7  .  ?        ?     ?  
 8  1  1  A   8  G    S    8  .  ?        ?     ?  
 9  1  1  A   9  A    S    9  .  ?        ?     ?  
10  1  1  A  10  C    S   10  .  ?        ?     ?  
11  1  2  B   1  DG   A    1  .  ?        1     ?  
12  1  2  B   2  DT   A    2  .  ?        ?     ?  
13  1  2  B   3  DC   A    3  .  ?        ?     ?  
14  1  2  B   4  DG   A    4  .  ?        ?     ?  
15  1  2  B   5  DG   A    5  .  ?        ?     1  
16  1  2  B   6  DC   A    6  .  ?        ?     1  
17  1  2  B   7  DC   A    7  .  ?        ?     ?  
18  1  2  B   8  DC   A    8  .  ?        ?     ?  
19  1  2  B   9  DA   A    9  .  ?        ?     ?  
20  1  2  B  10  DC   A   10  .  ?        ?     ?  
21  1  3  C   .  SO4  A  101  .  ?        ?     ?  
22  1  4  D   .  HOH  S  101  .  ?        ?     ?  
23  1  4  D   .  HOH  S  102  .  ?        ?     ?  
24  1  4  D   .  HOH  S  103  .  ?        ?     ?  
25  1  4  D   .  HOH  S  104  .  ?        ?     ?  
26  1  4  D   .  HOH  S  105  .  ?        ?     ?  
27  1  4  D   .  HOH  S  106  .  ?        ?     ?  
28  1  4  D   .  HOH  S  107  .  ?        ?     ?  
29  1  4  D   .  HOH  S  108  .  ?        ?     ?  
30  1  4  D   .  HOH  S  109  .  ?        ?     ?  
31  1  4  D   .  HOH  S  110  .  ?        ?     ?  
32  1  4  E   .  HOH  A  201  .  ?        ?     ?  
33  1  4  E   .  HOH  A  202  .  ?        ?     ?  
34  1  4  E   .  HOH  A  203  .  ?        ?     ?  
35  1  4  E   .  HOH  A  204  .  ?        ?     ?  
36  1  4  E   .  HOH  A  205  .  ?        ?     ?  
37  1  4  E   .  HOH  A  206  .  ?        ?     ?  
38  1  4  E   .  HOH  A  207  .  ?        ?     ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.RNA_score
_pdbx_vrpt_model_instance_geometry.RNA_suite
_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  0.00  NotAvailable    11  66.960    27  2.06    41  0.78  molprobity  1.000  
 2   2  0.79  Rotameric       10  42.890    22  0.47    34  1.05  molprobity  1.000  
 3   3  0.49  Rotameric       11  43.640    26  0.58    41  1.14  molprobity  1.000  
 4   4  0.34  Rotameric       11  42.070    26  0.52    41  0.91  molprobity  1.000  
 5   5  0.75  Rotameric       11  38.360    26  0.63    41  1.00  molprobity  1.000  
 6   6  0.91  Rotameric       11  38.690    22  0.56    34  0.94  molprobity  1.000  
 7   7  0.82  Rotameric       11  42.260    22  0.33    34  0.72  molprobity  1.000  
 8   8  0.00  NonRotameric    11  42.830    26  0.54    41  1.08  molprobity  1.000  
 9   9  0.57  Rotameric       11  40.880    25  0.59    39  1.00  molprobity  1.000  
10  10  0.96  Rotameric       12  37.770    21  0.37    30  0.87  molprobity  1.000  
11  11     ?  ?               11  59.830    26  2.20    39  0.70  molprobity  1.000  
12  12     ?  ?               12  43.680    22  0.63    34  1.34  molprobity  1.000  
13  13     ?  ?               11  43.450    21  0.54    32  0.60  molprobity  1.000  
14  14     ?  ?               11  37.540    25  0.64    39  0.97  molprobity  1.000  
15  15     ?  ?               11  38.430    25  1.01    39  0.65  molprobity  1.000  
16  16     ?  ?               11  39.940    21  0.71    32  0.98  molprobity  1.000  
17  17     ?  ?               11  41.060    21  0.76    32  1.12  molprobity  1.000  
18  18     ?  ?               11  38.780    21  0.93    32  0.67  molprobity  1.000  
19  19     ?  ?               11  41.210    24  1.02    37  1.07  molprobity  1.000  
20  20     ?  ?               12  49.670    20  0.82    28  0.99  molprobity  1.000  
21  21     ?  ?                ?  83.160     4  0.19     6  0.08  mogul       1.000  
22  22     ?  ?                ?  49.690     ?     ?     ?     ?  ?           1.000  
23  23     ?  ?                ?  45.040     ?     ?     ?     ?  ?           1.000  
24  24     ?  ?                ?  39.090     ?     ?     ?     ?  ?           1.000  
25  25     ?  ?                ?  50.420     ?     ?     ?     ?  ?           1.000  
26  26     ?  ?                ?  45.380     ?     ?     ?     ?  ?           1.000  
27  27     ?  ?                ?  47.260     ?     ?     ?     ?  ?           1.000  
28  28     ?  ?                ?  42.920     ?     ?     ?     ?  ?           1.000  
29  29     ?  ?                ?  53.820     ?     ?     ?     ?  ?           1.000  
30  30     ?  ?                ?  53.240     ?     ?     ?     ?  ?           1.000  
31  31     ?  ?                ?  48.030     ?     ?     ?     ?  ?           1.000  
32  32     ?  ?                ?  49.210     ?     ?     ?     ?  ?           1.000  
33  33     ?  ?                ?  54.720     ?     ?     ?     ?  ?           1.000  
34  34     ?  ?                ?  45.800     ?     ?     ?     ?  ?           1.000  
35  35     ?  ?                ?  38.380     ?     ?     ?     ?  ?           1.000  
36  36     ?  ?                ?  53.720     ?     ?     ?     ?  ?           1.000  
37  37     ?  ?                ?  41.240     ?     ?     ?     ?  ?           1.000  
38  38     ?  ?                ?  54.060     ?     ?     ?     ?  ?           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  15  "H2'"  1  0.49  2.48  
2  16  C6     1  0.49  2.48  
#
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   1  OP3  P  1.482  1.607  0.012  -10.46  
2  11  OP3  P  1.482  1.607  0.012  -10.41  
#
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  24  0.880  0.155   0.884  
 2   2  20  0.969  0.073  -0.703  
 3   3  23  0.918  0.113   0.107  
 4   4  23  0.911  0.101  -0.115  
 5   5  23  0.960  0.082  -0.466  
 6   6  20  0.970  0.073  -0.542  
 7   7  20  0.962  0.086  -0.359  
 8   8  23  0.917  0.091  -0.299  
 9   9  22  0.968  0.087  -0.446  
10  10  20  0.984  0.077  -0.486  
11  11  23  0.854  0.138   0.618  
12  12  20  0.962  0.089  -0.392  
13  13  19  0.942  0.106  -0.111  
14  14  22  0.970  0.092  -0.260  
15  15  22  0.956  0.094  -0.221  
16  16  19  0.934  0.093  -0.302  
17  17  19  0.940  0.096  -0.258  
18  18  19  0.953  0.084  -0.434  
19  19  21  0.965  0.075  -0.603  
20  20  19  0.949  0.090  -0.346  
21  21   5  0.666  0.314       ?  
22  22   1  0.904  0.184       ?  
23  23   1  0.963  0.221       ?  
24  24   1  0.963  0.370       ?  
25  25   1  0.808  0.146       ?  
26  26   1  0.865  0.123       ?  
27  27   1  0.817  0.181       ?  
28  28   1  0.954  0.313       ?  
29  29   1  0.870  0.487       ?  
30  30   1  0.587  0.227       ?  
31  31   1  0.894  0.314       ?  
32  32   1  0.934  0.189       ?  
33  33   1  0.808  0.144       ?  
34  34   1  0.962  0.154       ?  
35  35   1  0.890  0.111       ?  
36  36   1  0.931  0.249       ?  
37  37   1  0.947  0.357       ?  
38  38   1  0.618  0.187       ?  
#
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        "1.8.5 (274361), CSD as541be (2020)"                                  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  
##
