data_6AR5

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  6AR5
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    6AR5
_pdbx_vrpt_summary.PDB_deposition_date         2017-08-21
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2024-03-13
_pdbx_vrpt_summary.RNA_suiteness               0.76
_pdbx_vrpt_summary.report_creation_date        2024-06-24:11:31
_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    
2  polymer  RNA    
3  water    water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
D  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all    x-ray  
2  2.413  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   94.84  141614     ?     ?  
2  2  1   96.98    5161  2.40  2.44  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    4543  2.40  2.44  
5  1  3   77.02  130704     ?     ?  
6  2  3   94.56    4647  2.40  2.44  
7  1  4   90.78    3102     ?     ?  
8  2  4   93.80    1080  2.04  2.80  
#
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  0.95  0.90  291  446  
2  1  2  B  B  1.05  0.53  330  513  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       1.17
_pdbx_vrpt_summary_geometry.num_H_reduce     297
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   621
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.73
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  959
_pdbx_vrpt_summary_geometry.angles_RMSZ      1.01
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 99.434
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            26.258
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         46.337
_pdbx_vrpt_summary_diffraction.I_over_sigma              6.49(2.42A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        4250
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.500
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.327
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.485
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.319
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.954
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.056
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.21
_pdbx_vrpt_summary_diffraction.EDS_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.41
_pdbx_vrpt_summary_diffraction.EDS_res_low               36.12
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[51.824,51.824,37.636,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.301
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 10.34% 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         99.98
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      212
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.99
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.41
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        36.12
_pdbx_vrpt_summary_diffraction.PDB_R                     0.19
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.21
#
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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  DG   A    1  .  ?        ?     ?  
 2  1  1  A   2  DT   A    2  .  ?        ?     ?  
 3  1  1  A   3  DC   A    3  .  ?        ?     ?  
 4  1  1  A   4  DT   A    4  .  ?        ?     ?  
 5  1  1  A   5  DC   A    5  .  ?        ?     ?  
 6  1  1  A   6  DC   A    6  .  ?        ?     ?  
 7  1  1  A   7  DA   A    7  .  ?        ?     ?  
 8  1  1  A   8  DG   A    8  .  ?        ?     ?  
 9  1  1  A   9  DG   A    9  .  ?        ?     ?  
10  1  1  A  10  DC   A   10  .  ?        ?     ?  
11  1  1  A  11  DA   A   11  .  ?        ?     1  
12  1  1  A  12  DA   A   12  .  ?        ?     1  
13  1  1  A  13  DC   A   13  .  ?        ?     ?  
14  1  2  B   1  U    B    1  .  ?        ?     ?  
15  1  2  B   2  G    B    2  .  ?        ?     ?  
16  1  2  B   3  U    B    3  .  ?        ?     ?  
17  1  2  B   4  U    B    4  .  ?        ?     ?  
18  1  2  B   5  G    B    5  .  ?        ?     ?  
19  1  2  B   6  C    B    6  .  ?        ?     ?  
20  1  2  B   7  C    B    7  .  ?        ?     ?  
21  1  2  B   8  U    B    8  .  ?        ?     ?  
22  1  2  B   9  G    B    9  .  ?        1     ?  
23  1  2  B  10  G    B   10  .  ?        ?     ?  
24  1  2  B  11  A    B   11  .  ?        ?     ?  
25  1  2  B  12  G    B   12  .  ?        ?     ?  
26  1  2  B  13  A    B   13  .  ?        ?     ?  
27  1  2  B  14  C    B   14  .  ?        ?     ?  
28  1  3  C   .  HOH  A  101  .  ?        ?     ?  
29  1  3  C   .  HOH  A  102  .  ?        ?     ?  
30  1  3  C   .  HOH  A  103  .  ?        ?     ?  
31  1  3  C   .  HOH  A  104  .  ?        ?     ?  
32  1  3  D   .  HOH  B  101  .  ?        ?     ?  
33  1  3  D   .  HOH  B  102  .  ?        ?     ?  
34  1  3  D   .  HOH  B  103  .  ?        ?     ?  
35  1  3  D   .  HOH  B  104  .  ?        ?     ?  
36  1  3  D   .  HOH  B  105  .  ?        ?     ?  
37  1  3  D   .  HOH  B  106  .  ?        ?     ?  
38  1  3  D   .  HOH  B  107  .  ?        ?     ?  
39  1  3  D   .  HOH  B  108  .  ?        ?     ?  
40  1  3  D   .  HOH  B  109  .  ?        ?     ?  
41  1  3  D   .  HOH  B  110  .  ?        ?     ?  
42  1  3  D   .  HOH  B  111  .  ?        ?     ?  
43  1  3  D   .  HOH  B  112  .  ?        ?     ?  
44  1  3  D   .  HOH  B  113  .  ?        ?     ?  
45  1  3  D   .  HOH  B  114  .  ?        ?     ?  
46  1  3  D   .  HOH  B  115  .  ?        ?     ?  
47  1  3  D   .  HOH  B  116  .  ?        ?     ?  
48  1  3  D   .  HOH  B  117  .  ?        ?     ?  
#
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     ?  ?               12  41.220    22  1.13    35  0.44  molprobity  1.000  
 2   2     ?  ?               12  40.150    22  0.99    34  1.29  molprobity  1.000  
 3   3     ?  ?               11  37.470    21  0.73    32  0.98  molprobity  1.000  
 4   4     ?  ?               12  36.070    22  0.72    34  1.43  molprobity  1.000  
 5   5     ?  ?               11  35.390    21  0.70    32  1.11  molprobity  1.000  
 6   6     ?  ?               11  37.640    21  0.84    32  0.98  molprobity  1.000  
 7   7     ?  ?               11  40.880    24  1.08    37  0.65  molprobity  1.000  
 8   8     ?  ?               11  39.950    25  0.72    39  0.88  molprobity  1.000  
 9   9     ?  ?               11  36.690    25  1.12    39  0.77  molprobity  1.000  
10  10     ?  ?               11  36.510    21  1.06    32  0.90  molprobity  1.000  
11  11     ?  ?               11  42.470    24  0.71    37  0.86  molprobity  1.000  
12  12     ?  ?               11  43.610    24  1.01    37  0.78  molprobity  1.000  
13  13     ?  ?               10  48.660    19  0.53    26  1.06  molprobity  1.000  
14  14  0.00  NotAvailable    11  60.770    19  0.81    30  1.40  molprobity  1.000  
15  15  0.47  Rotameric       11  39.950    26  0.36    41  0.72  molprobity  1.000  
16  16  0.91  Rotameric       10  37.540    22  0.37    34  0.92  molprobity  1.000  
17  17  0.86  Rotameric       10  40.080    22  0.50    34  0.85  molprobity  1.000  
18  18  0.91  Rotameric       11  40.480    26  0.49    41  0.95  molprobity  1.000  
19  19  0.69  Rotameric       11  40.920    22  0.39    34  0.95  molprobity  1.000  
20  20  0.88  Rotameric       11  39.330    22  0.44    34  0.99  molprobity  1.000  
21  21  0.73  Rotameric       10  39.260    22  0.51    34  1.19  molprobity  1.000  
22  22  0.92  Rotameric       11  38.300    26  0.80    41  1.69  molprobity  1.000  
23  23  0.73  Rotameric       11  37.690    26  0.59    41  1.11  molprobity  1.000  
24  24  0.72  Rotameric       11  37.780    25  0.52    39  0.92  molprobity  1.000  
25  25  0.35  Rotameric       11  36.870    26  0.41    41  0.88  molprobity  1.000  
26  26  0.79  Rotameric       11  39.090    25  0.59    39  0.87  molprobity  1.000  
27  27  0.88  Rotameric       12  36.590    21  0.36    30  0.76  molprobity  1.000  
28  28     ?  ?                ?  28.640     ?     ?     ?     ?  ?           1.000  
29  29     ?  ?                ?  31.120     ?     ?     ?     ?  ?           1.000  
30  30     ?  ?                ?  41.000     ?     ?     ?     ?  ?           1.000  
31  31     ?  ?                ?  42.090     ?     ?     ?     ?  ?           1.000  
32  32     ?  ?                ?  38.880     ?     ?     ?     ?  ?           1.000  
33  33     ?  ?                ?  33.450     ?     ?     ?     ?  ?           1.000  
34  34     ?  ?                ?  38.340     ?     ?     ?     ?  ?           1.000  
35  35     ?  ?                ?  38.370     ?     ?     ?     ?  ?           1.000  
36  36     ?  ?                ?  47.920     ?     ?     ?     ?  ?           1.000  
37  37     ?  ?                ?  41.770     ?     ?     ?     ?  ?           1.000  
38  38     ?  ?                ?  32.980     ?     ?     ?     ?  ?           1.000  
39  39     ?  ?                ?  38.250     ?     ?     ?     ?  ?           1.000  
40  40     ?  ?                ?  37.660     ?     ?     ?     ?  ?           1.000  
41  41     ?  ?                ?  35.280     ?     ?     ?     ?  ?           1.000  
42  42     ?  ?                ?  43.630     ?     ?     ?     ?  ?           1.000  
43  43     ?  ?                ?  34.210     ?     ?     ?     ?  ?           1.000  
44  44     ?  ?                ?  43.020     ?     ?     ?     ?  ?           1.000  
45  45     ?  ?                ?  36.370     ?     ?     ?     ?  ?           1.000  
46  46     ?  ?                ?  44.350     ?     ?     ?     ?  ?           1.000  
47  47     ?  ?                ?  40.520     ?     ?     ?     ?  ?           1.000  
48  48     ?  ?                ?  43.730     ?     ?     ?     ?  ?           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  11  "H2'"  1  0.41  2.55  
2  12  C8     1  0.41  2.55  
#
_pdbx_vrpt_instance_intra_angle_outliers.ordinal      1
_pdbx_vrpt_instance_intra_angle_outliers.instance_id  22
_pdbx_vrpt_instance_intra_angle_outliers.atom_1       N3
_pdbx_vrpt_instance_intra_angle_outliers.atom_2       C2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3       N2
_pdbx_vrpt_instance_intra_angle_outliers.obs          116.354
_pdbx_vrpt_instance_intra_angle_outliers.mean         119.900
_pdbx_vrpt_instance_intra_angle_outliers.stdev        0.700
_pdbx_vrpt_instance_intra_angle_outliers.Z            -5.07
#
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  0.966  0.133  -0.472  
 2   2  20  0.972  0.146  -0.357  
 3   3  19  0.977  0.138  -0.406  
 4   4  20  0.971  0.145  -0.371  
 5   5  19  0.979  0.145  -0.290  
 6   6  19  0.968  0.134  -0.472  
 7   7  21  0.971  0.123  -0.663  
 8   8  22  0.961  0.116  -0.771  
 9   9  22  0.973  0.144  -0.278  
10  10  19  0.985  0.120  -0.703  
11  11  21  0.956  0.127  -0.602  
12  12  21  0.972  0.151  -0.236  
13  13  18  0.963  0.165   0.040  
14  14  17  0.910  0.240   1.128  
15  15  23  0.978  0.147  -0.472  
16  16  20  0.968  0.135  -0.622  
17  17  20  0.953  0.157  -0.255  
18  18  23  0.956  0.136  -0.697  
19  19  20  0.959  0.122  -0.938  
20  20  20  0.971  0.118  -1.013  
21  21  20  0.978  0.119  -0.888  
22  22  23  0.975  0.138  -0.656  
23  23  23  0.964  0.121  -1.004  
24  24  22  0.966  0.121  -0.989  
25  25  23  0.953  0.143  -0.554  
26  26  22  0.974  0.146  -0.512  
27  27  20  0.966  0.142  -0.565  
28  28   1  0.902  0.282       ?  
29  29   1  0.943  0.115       ?  
30  30   1  0.738  0.269       ?  
31  31   1  0.944  0.164       ?  
32  32   1  0.896  0.408       ?  
33  33   1  0.985  0.369       ?  
34  34   1  0.976  0.428       ?  
35  35   1  0.789  0.171       ?  
36  36   1  0.851  0.432       ?  
37  37   1  0.711  0.277       ?  
38  38   1  0.934  0.181       ?  
39  39   1  0.969  0.252       ?  
40  40   1  0.872  0.107       ?  
41  41   1  0.978  0.225       ?  
42  42   1  0.891  0.210       ?  
43  43   1  0.977  0.230       ?  
44  44   1  0.847  0.255       ?  
45  45   1  0.956  0.113       ?  
46  46   1  0.865  0.286       ?  
47  47   1  0.901  0.088       ?  
48  48   1  0.891  0.169       ?  
#
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          2.37.1                                                                Y  
3  dcc          '"2.27  (2023-04-10)"'                                                Y  
4  xtriage      1.20.1                                                                Y  
5  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
