data_7WII

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7WII
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7WII
_pdbx_vrpt_summary.PDB_deposition_date         2022-01-03
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2023-01-18
_pdbx_vrpt_summary.RNA_suiteness               0.64
_pdbx_vrpt_summary.report_creation_date        2023-01-11:11:16
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,buster-report,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   Y
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "RNA (50-MER)"  
2  non-polymer  2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE  
#
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  2.75  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  19.58  141614     ?     ?  
2  2  1  30.54    1277  2.74  2.78  
3  1  2  36.85  127900     ?     ?  
4  2  2  44.24    1207  2.74  2.78  
5  1  3  57.97  130704     ?     ?  
6  2  3  89.97    1235  2.74  2.78  
7  1  4  72.11    3102     ?     ?  
8  2  4  78.49    1060  2.50  3.02  
#
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  V  36.85  
2  4  2  A  1  1  V  44.24  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     V
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      0.66
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.13
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   1170
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  1822
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       12.73
_pdbx_vrpt_summary_geometry.num_H_reduce     555
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   1170
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.13
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1822
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.66
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 145.799
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            54.500
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         88.693
_pdbx_vrpt_summary_diffraction.I_over_sigma              3.83(2.76A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        6473
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.467
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.206
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.482
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.316
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.963
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.028
_pdbx_vrpt_summary_diffraction.DCC_R                     0.20
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.23
_pdbx_vrpt_summary_diffraction.EDS_R                     0.21
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.75
_pdbx_vrpt_summary_diffraction.EDS_res_low               33.30
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[78.323,78.323,139.856,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.623
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 5.87% 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         98.73
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      641
_pdbx_vrpt_summary_diffraction.percent_free_reflections  9.90
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     4.08
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.75
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        33.30
_pdbx_vrpt_summary_diffraction.PDB_R                     0.21
_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_clashes
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A   1  GTP  V    6  .  ?        ?  ?     
 2  1  1  A   2  G    V    7  .  ?        ?  ?     
 3  1  1  A   3  C    V    8  .  ?        1  ?     
 4  1  1  A   4  G    V    9  .  ?        1  ?     
 5  1  1  A   5  U    V   10  .  ?        1  ?     
 6  1  1  A   6  G    V   11  .  ?        3  ?     
 7  1  1  A   7  G    V   12  .  ?        3  ?     
 8  1  1  A   8  U    V   13  .  ?        1  ?     
 9  1  1  A   9  C    V   14  .  ?        1  ?     
10  1  1  A  10  C    V   15  .  ?        ?  ?     
11  1  1  A  11  G    V   16  .  ?        ?  ?     
12  1  1  A  12  U    V   17  .  ?        ?  ?     
13  1  1  A  13  U    V   18  .  ?        ?  ?     
14  1  1  A  14  C    V   19  .  ?        ?  ?     
15  1  1  A  15  A    V   20  .  ?        ?  ?     
16  1  1  A  16  A    V   21  .  ?        ?  ?     
17  1  1  A  17  C    V   22  .  ?        ?  ?     
18  1  1  A  18  U    V   23  .  ?        ?  ?     
19  1  1  A  19  C    V   24  .  ?        2  ?     
20  1  1  A  20  G    V   25  .  ?        2  ?     
21  1  1  A  21  U    V   26  .  ?        ?  ?     
22  1  1  A  22  U    V   27  .  ?        1  ?     
23  1  1  A  23  C    V   28  .  ?        4  ?     
24  1  1  A  24  C    V   29  .  ?        3  ?     
25  1  1  A  25  U    V   30  .  ?        ?  ?     
26  1  1  A  26  C    V   31  .  ?        ?  ?     
27  1  1  A  27  G    V   32  .  ?        ?  ?     
28  1  1  A  28  A    V   33  .  ?        2  ?     
29  1  1  A  29  A    V   34  .  ?        ?  ?     
30  1  1  A  30  A    V   35  .  ?        ?  ?     
31  1  1  A  31  G    V   37  .  ?        ?  ?     
32  1  1  A  32  A    V   38  .  ?        ?  ?     
33  1  1  A  33  G    V   39  .  ?        ?  ?     
34  1  1  A  34  G    V   40  .  ?        ?  ?     
35  1  1  A  35  A    V   41  .  ?        1  ?     
36  1  1  A  36  A    V   42  .  ?        3  ?     
37  1  1  A  37  C    V   43  .  ?        4  ?     
38  1  1  A  38  U    V   44  .  ?        5  ?     
39  1  1  A  39  A    V   45  .  ?        3  ?     
40  1  1  A  40  C    V   46  .  ?        ?  ?     
41  1  1  A  41  G    V   47  .  ?        ?  ?     
42  1  1  A  42  G    V   48  .  ?        ?  ?     
43  1  1  A  43  G    V   49  .  ?        ?  ?     
44  1  1  A  44  A    V   50  .  ?        1  ?     
45  1  1  A  45  G    V   51  .  ?        ?  ?     
46  1  1  A  46  A    V   52  .  ?        ?  ?     
47  1  1  A  47  C    V   53  .  ?        ?  ?     
48  1  1  A  48  G    V   54  .  ?        ?  ?     
49  1  1  A  49  C    V   55  .  ?        ?  ?     
50  1  1  A  50  C    V   56  .  ?        ?  ?     
51  1  2  B   .  NPR  V  101  .  ?        ?  Y     
#
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     ?  ?                  11  137.190     ?     ?     ?     ?  ?           1.000  
 2   2  0.00  NotAvailable       11  114.600    26  0.14    41  0.62  molprobity  1.000  
 3   3  0.91  Rotameric          11  118.030    22  0.09    34  0.68  molprobity  1.000  
 4   4  0.82  Rotameric          11  113.720    26  0.13    41  0.61  molprobity  1.000  
 5   5  0.73  Rotameric          10  112.650    22  0.10    34  0.66  molprobity  1.000  
 6   6  0.28  Rotameric          11  109.830    26  0.24    41  0.99  molprobity  1.000  
 7   7  0.12  Rotameric          11  100.060    26  0.17    41  0.65  molprobity  1.000  
 8   8  0.66  Rotameric          10   92.730    22  0.10    34  0.67  molprobity  1.000  
 9   9  0.73  Rotameric          11   85.810    22  0.11    34  0.69  molprobity  1.000  
10  10  0.88  Rotameric          11   82.920    22  0.09    34  0.69  molprobity  1.000  
11  11  0.96  Rotameric          11   77.950    26  0.16    41  0.67  molprobity  1.000  
12  12  0.14  Rotameric          10   85.410    22  0.14    34  0.70  molprobity  1.000  
13  13  0.00  Triaged/NotBinned  10  168.080    22  0.09    34  0.69  molprobity  1.000  
14  14  0.00  NonRotameric       11  179.780    22  0.12    34  0.62  molprobity  1.000  
15  15  0.00  NonRotameric       11   97.810    25  0.15    39  0.66  molprobity  1.000  
16  16  0.94  Rotameric          11   83.470    25  0.14    39  0.62  molprobity  1.000  
17  17  0.71  Rotameric          11   88.740    22  0.08    34  0.68  molprobity  1.000  
18  18  0.64  Rotameric          10   93.980    22  0.10    34  0.65  molprobity  1.000  
19  19  0.17  Rotameric          11  125.900    22  0.15    34  0.64  molprobity  1.000  
20  20  0.00  Triaged/NotBinned  11   87.240    26  0.12    41  0.59  molprobity  1.000  
21  21  0.95  Rotameric          10   95.360    22  0.08    34  0.69  molprobity  1.000  
22  22  0.99  Rotameric          10  103.990    22  0.09    34  0.70  molprobity  1.000  
23  23  0.86  Rotameric          11  104.260    22  0.09    34  0.72  molprobity  1.000  
24  24  0.84  Rotameric          11  101.440    22  0.07    34  0.66  molprobity  1.000  
25  25  0.92  Rotameric          10   89.160    22  0.08    34  0.66  molprobity  1.000  
26  26  0.76  Rotameric          11   85.570    22  0.08    34  0.65  molprobity  1.000  
27  27  0.80  Rotameric          11   82.540    26  0.14    41  0.66  molprobity  1.000  
28  28  0.28  Rotameric          11   81.620    25  0.13    39  0.66  molprobity  1.000  
29  29  0.88  Rotameric          11   77.080    25  0.17    39  0.69  molprobity  1.000  
30  30  0.94  Rotameric          11   74.590    25  0.16    39  0.66  molprobity  1.000  
31  31  0.30  Rotameric          11   75.190    26  0.13    41  0.63  molprobity  1.000  
32  32  0.89  Rotameric          11   77.900    25  0.14    39  0.62  molprobity  1.000  
33  33  0.87  Rotameric          11   87.100    26  0.15    41  0.64  molprobity  1.000  
34  34  0.00  NonRotameric       11   94.570    26  0.16    41  0.60  molprobity  1.000  
35  35  0.56  Rotameric          11   94.910    25  0.15    39  0.62  molprobity  1.000  
36  36  0.80  Rotameric          11   93.720    25  0.13    39  0.62  molprobity  1.000  
37  37  0.82  Rotameric          11   93.890    22  0.10    34  0.65  molprobity  1.000  
38  38  0.80  Rotameric          10   90.280    22  0.11    34  0.70  molprobity  1.000  
39  39  0.71  Rotameric          11   87.360    25  0.20    39  0.78  molprobity  1.000  
40  40  0.11  Rotameric          11   76.960    22  0.16    34  0.64  molprobity  1.000  
41  41  0.27  Rotameric          11   74.480    26  0.18    41  0.66  molprobity  1.000  
42  42  0.04  Rotameric          11   75.800    26  0.12    41  0.57  molprobity  1.000  
43  43  0.78  Rotameric          11   78.160    26  0.14    41  0.62  molprobity  1.000  
44  44  0.97  Rotameric          11   83.590    25  0.15    39  0.61  molprobity  1.000  
45  45  0.06  Rotameric          11   94.110    26  0.15    41  0.66  molprobity  1.000  
46  46  0.85  Rotameric          11  105.860    25  0.13    39  0.60  molprobity  1.000  
47  47  0.96  Rotameric          11  122.190    22  0.08    34  0.67  molprobity  1.000  
48  48  0.97  Rotameric          11  120.460    26  0.15    41  0.63  molprobity  1.000  
49  49  0.95  Rotameric          11  124.760    22  0.09    34  0.69  molprobity  1.000  
50  50  0.90  Rotameric          12  132.640    21  0.10    30  0.65  molprobity  1.000  
51  51     ?  ?                  13   90.720    14  0.70    13  1.07  mogul       0.911  
#
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   3  "O2'"    1  0.47  2.15  
 2   4  "H5'"    1  0.47  2.15  
 3   5  "O2'"    2  0.56  2.06  
 4   6  "H5'"    2  0.56  2.06  
 5   6  "H2'"    3  0.51  2.10  
 6   6  "H2'"    4  0.47  2.49  
 7   7  "O4'"    3  0.51  2.10  
 8   7  H22      5  0.50  1.60  
 9   7  C8       4  0.47  2.49  
10   8  "H2'"    6  0.62  2.35  
11   9  C6       6  0.62  2.35  
12  19  "H3'"    7  0.57  1.87  
13  19  "H3'"    8  0.44  2.44  
14  20  "H5''"   7  0.57  1.87  
15  20  "C5'"    8  0.44  2.44  
16  22  "O2'"    9  0.45  2.16  
17  23  "H2'"   10  0.48  1.78  
18  23  "H2'"   11  0.46  2.50  
19  23  "H5'"    9  0.45  2.16  
20  23  "O2'"   12  0.43  2.18  
21  24  H6      10  0.48  1.78  
22  24  C6      11  0.46  2.50  
23  24  "H5'"   12  0.43  2.18  
24  28  OP1     13  0.44  2.01  
25  28  H8      13  0.44  2.01  
26  35  "O2'"   14  0.49  2.12  
27  36  "H5'"   14  0.49  2.12  
28  36  "O2'"   15  0.48  2.14  
29  36  "H2'"   16  0.44  2.52  
30  37  "H2'"   17  0.53  2.44  
31  37  "H2'"   18  0.42  2.19  
32  37  "H5'"   15  0.48  2.14  
33  37  C6      16  0.44  2.52  
34  38  "C2'"   19  0.61  2.31  
35  38  C6      17  0.53  2.44  
36  38  "O2'"   20  0.52  2.08  
37  38  "H2'"   21  0.44  1.99  
38  38  "O4'"   18  0.42  2.19  
39  39  "H5'"   19  0.61  2.31  
40  39  "H5'"   20  0.52  2.08  
41  39  "H5'"   21  0.44  1.99  
42  44  H2       5  0.50  1.60  
#
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  32  0.868  0.138       ?  
 2   2  23  0.876  0.109  -1.252  
 3   3  20  0.899  0.185   0.099  
 4   4  23  0.929  0.144  -0.584  
 5   5  20  0.952  0.115  -1.056  
 6   6  23  0.925  0.155  -0.374  
 7   7  23  0.941  0.155  -0.374  
 8   8  20  0.964  0.158  -0.342  
 9   9  20  0.961  0.182   0.046  
10  10  20  0.974  0.200   0.365  
11  11  23  0.970  0.224   0.943  
12  12  20  0.934  0.221   0.704  
13  13  20  0.808  0.298   1.983  
14  14  20  0.801  0.328   2.630  
15  15  22  0.916  0.174  -0.125  
16  16  22  0.952  0.149  -0.589  
17  17  20  0.931  0.183   0.064  
18  18  20  0.933  0.156  -0.375  
19  19  20  0.939  0.183   0.064  
20  20  23  0.927  0.159  -0.298  
21  21  20  0.953  0.145  -0.558  
22  22  20  0.874  0.174  -0.076  
23  23  20  0.941  0.173  -0.113  
24  24  20  0.892  0.159  -0.361  
25  25  20  0.945  0.185   0.106  
26  26  20  0.955  0.200   0.365  
27  27  23  0.940  0.170  -0.088  
28  28  22  0.943  0.206   0.470  
29  29  22  0.967  0.187   0.117  
30  30  22  0.954  0.195   0.266  
31  31  23  0.945  0.206   0.599  
32  32  22  0.900  0.224   0.805  
33  33  23  0.887  0.178   0.065  
34  34  23  0.884  0.150  -0.469  
35  35  22  0.902  0.151  -0.552  
36  36  22  0.922  0.162  -0.348  
37  37  20  0.939  0.146  -0.591  
38  38  20  0.925  0.140  -0.641  
39  39  22  0.922  0.179  -0.032  
40  40  20  0.960  0.162  -0.308  
41  41  23  0.968  0.180   0.103  
42  42  23  0.967  0.208   0.637  
43  43  23  0.968  0.200   0.485  
44  44  22  0.958  0.209   0.526  
45  45  23  0.933  0.158  -0.317  
46  46  22  0.915  0.166  -0.273  
47  47  20  0.879  0.139  -0.715  
48  48  23  0.835  0.130  -0.851  
49  49  20  0.835  0.177  -0.042  
50  50  20  0.876  0.297   2.081  
51  51  17  0.946  0.180       ?  
#
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          2.31.3                                                                Y  
4  dcc          "2.26  (2020-01-20)"                                                  Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
