data_7OZZ

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7OZZ
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7OZZ
_pdbx_vrpt_summary.PDB_deposition_date         2021-06-29
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2023-03-15
_pdbx_vrpt_summary.RNA_suiteness               0.73
_pdbx_vrpt_summary.report_creation_date        2023-03-09:15:21
_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(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3')"  
2  polymer      "DNA (5'-D(*CP*TP*(05H)P*TP*CP*TP*TP*TP*G)-3')"  
3  non-polymer  "POTASSIUM ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  x-ray  
2  2.7  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   74.38  141614     ?     ?  
2  2  1   87.16    3122  2.70  2.70  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    2737  2.70  2.70  
5  1  3   46.99  130704     ?     ?  
6  2  3   79.68    2808  2.70  2.70  
7  1  4   88.07    3102     ?     ?  
8  2  4   93.96    1159  2.40  3.00  
#
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  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  0.69  0.41  245  381  
2  1  2  B  B  1.04  0.63  172  261  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       3.21
_pdbx_vrpt_summary_geometry.num_H_reduce     207
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   417
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.51
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  642
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.85
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 145.189
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            65.536
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         102.117
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.26(2.72A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2269
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.430
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.245
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.490
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.329
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.961
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.068
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.70
_pdbx_vrpt_summary_diffraction.EDS_res_low               27.06
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[92.773,92.773,124.227,-0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.305
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 7.42% 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         99.87
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      137
_pdbx_vrpt_summary_diffraction.percent_free_reflections  6.00
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.70
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        27.06
_pdbx_vrpt_summary_diffraction.PDB_R                     0.20
_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.count_mogul_bond_outliers
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A   1  C    A    1  .  ?        ?     ?     ?     ?  ?     
 2  1  1  A   2  A    A    2  .  ?        ?     ?     ?     ?  ?     
 3  1  1  A   3  A    A    3  .  ?        ?     ?     ?     ?  ?     
 4  1  1  A   4  A    A    4  .  ?        2     ?     ?     ?  ?     
 5  1  1  A   5  G    A    5  .  ?        2     ?     ?     ?  ?     
 6  1  1  A   6  A    A    6  .  ?        ?     ?     ?     ?  ?     
 7  1  1  A   7  A    A    7  .  ?        ?     ?     ?     ?  ?     
 8  1  1  A   8  A    A    8  .  ?        ?     ?     ?     ?  ?     
 9  1  1  A   9  A    A    9  .  ?        ?     ?     ?     ?  ?     
10  1  1  A  10  G    A   10  .  ?        ?     ?     ?     ?  ?     
11  1  2  B   1  DC   B   11  .  ?        ?     ?     ?     ?  ?     
12  1  2  B   2  DT   B   12  .  ?        ?     ?     ?     ?  ?     
13  1  2  B   3  05H  B   13  .  ?        ?    10    18     2  Y     
14  1  2  B   4  DT   B   14  .  ?        ?     ?     ?     ?  ?     
15  1  2  B   5  DC   B   15  .  ?        ?     ?     ?     ?  ?     
16  1  2  B   6  DT   B   16  .  ?        ?     ?     ?     ?  ?     
17  1  2  B   7  DT   B   17  .  ?        ?     ?     ?     ?  ?     
18  1  2  B   8  DT   B   18  .  ?        ?     ?     ?     ?  ?     
19  1  2  B   9  DG   B   19  .  ?        ?     ?     ?     ?  ?     
20  1  3  C   .  K    A  101  .  ?        ?     ?     ?     ?  ?     
#
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    12  117.970    19  0.24    30  0.52  molprobity  1.000  
 2   2  0.66  Rotameric       11  107.770    25  0.32    39  0.58  molprobity  1.000  
 3   3  0.95  Rotameric       11   97.580    25  0.30    39  0.73  molprobity  1.000  
 4   4  0.94  Rotameric       11   93.470    25  0.32    39  0.65  molprobity  1.000  
 5   5  0.86  Rotameric       11   95.000    26  0.39    41  0.78  molprobity  1.000  
 6   6  0.69  Rotameric       11   95.530    25  0.62    39  0.86  molprobity  1.000  
 7   7  0.25  Rotameric       11   98.610    25  0.39    39  0.49  molprobity  1.000  
 8   8  0.58  Rotameric       11  100.800    25  0.52    39  0.74  molprobity  1.000  
 9   9  0.82  Rotameric       11   95.160    25  0.39    39  0.65  molprobity  1.000  
10  10  0.83  Rotameric       12   88.450    25  0.39    37  0.75  molprobity  1.000  
11  11     ?  ?               12  103.790    18  0.80    28  0.80  molprobity  1.000  
12  12     ?  ?               12  104.340    21  0.29    30  0.40  molprobity  1.000  
13  13     ?  ?                ?   98.330    42  1.50    55  2.32  mogul       1.000  
14  14     ?  ?               12   92.430    22  0.72    34  1.36  molprobity  1.000  
15  15     ?  ?               11   94.390    21  0.71    32  0.80  molprobity  1.000  
16  16     ?  ?               12   91.300    22  0.54    34  1.21  molprobity  1.000  
17  17     ?  ?               12   86.070    22  0.57    34  1.24  molprobity  1.000  
18  18     ?  ?               12   88.980    22  0.77    34  1.30  molprobity  1.000  
19  19     ?  ?               12   95.150    24  0.56    35  0.65  molprobity  1.000  
20  20     ?  ?                ?  152.670     ?     ?     ?     ?  ?           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  4  "H2'"  1  0.47  1.79  
2  4  "H2'"  2  0.47  2.50  
3  5  H8     1  0.47  1.79  
4  5  C8     2  0.47  2.50  
#
loop_
_pdbx_vrpt_instance_mogul_bond_outliers.ordinal
_pdbx_vrpt_instance_mogul_bond_outliers.instance_id
_pdbx_vrpt_instance_mogul_bond_outliers.atom_1
_pdbx_vrpt_instance_mogul_bond_outliers.atom_2
_pdbx_vrpt_instance_mogul_bond_outliers.obsval
_pdbx_vrpt_instance_mogul_bond_outliers.mean
_pdbx_vrpt_instance_mogul_bond_outliers.numobs
_pdbx_vrpt_instance_mogul_bond_outliers.stdev
_pdbx_vrpt_instance_mogul_bond_outliers.Zscore
_pdbx_vrpt_instance_mogul_bond_outliers.mindiff
 1  13  C2      N1      1.42  1.38   963  0.02   2.30  0.00  
 2  13  C2      N3      1.33  1.38  2449  0.02  -2.35  0.00  
 3  13  C21     N11     1.42  1.38   963  0.02   2.60  0.00  
 4  13  C21     N31     1.33  1.38  2449  0.02  -2.72  0.00  
 5  13  C4      N3      1.33  1.38  3597  0.02  -3.08  0.00  
 6  13  C41     N31     1.33  1.38  3597  0.02  -3.05  0.00  
 7  13  C6      C5      1.38  1.34   855  0.02   2.22  0.00  
 8  13  C6      N1      1.34  1.38   917  0.02  -2.32  0.00  
 9  13  "C3'1"  "C2'1"  1.49  1.53   174  0.02  -2.51  0.00  
10  13  "C4'1"  "C3'1"  1.49  1.54    52  0.02  -2.31  0.00  
#
loop_
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3
_pdbx_vrpt_instance_mogul_angle_outliers.obsval
_pdbx_vrpt_instance_mogul_angle_outliers.mean
_pdbx_vrpt_instance_mogul_angle_outliers.numobs
_pdbx_vrpt_instance_mogul_angle_outliers.stdev
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff
 1  13  N3      C2      N1      121.11  114.89   961  1.33   4.69  0.61  
 2  13  O2      C2      N3      116.94  121.50  2451  1.86  -2.45  0.02  
 3  13  N31     C21     N11     121.47  114.89   961  1.33   4.96  0.97  
 4  13  O21     C21     N31     115.57  121.50  2451  1.86  -3.19  0.08  
 5  13  C5      C4      N3      118.64  115.31   629  0.85   3.90  0.02  
 6  13  O4      C4      C5      120.72  124.90   632  1.16  -3.61  0.23  
 7  13  "C5'"   "C4'"   "C3'"   108.49  115.54    22  2.14  -3.29  2.77  
 8  13  C51     C41     N31     119.36  115.31   629  0.85   4.75  0.16  
 9  13  O41     C41     C51     119.80  124.90   632  1.16  -4.40  0.44  
10  13  "C4'"   "C5'"   "N5'"   103.80  112.69    51  1.97  -4.52  4.99  
11  13  C5      C6      N1      120.47  123.34   431  1.03  -2.78  0.06  
12  13  C51     C61     N11     119.72  123.34   431  1.03  -3.51  0.10  
13  13  "C3'1"  C11     C1      106.77  113.98   143  2.49  -2.89  0.52  
14  13  "C1'"   N1      C2      122.33  117.64   470  1.97   2.38  0.25  
15  13  C4      N3      C2      121.62  127.35  1185  1.30  -4.42  0.00  
16  13  C41     N31     C21     120.87  127.35  1185  1.30  -5.00  0.21  
17  13  "O4'1"  "C1'1"  N11     111.36  108.77    74  1.29   2.02  0.04  
18  13  "O4'1"  "C4'1"  "C5'1"  116.17  108.82    30  2.97   2.48  4.06  
#
loop_
_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal
_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_1
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_2
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_3
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_4
_pdbx_vrpt_instance_mogul_torsion_outliers.obsval
_pdbx_vrpt_instance_mogul_torsion_outliers.mean
_pdbx_vrpt_instance_mogul_torsion_outliers.numobs
_pdbx_vrpt_instance_mogul_torsion_outliers.stdev
_pdbx_vrpt_instance_mogul_torsion_outliers.mindiff
_pdbx_vrpt_instance_mogul_torsion_outliers.local_density
1  13  C1  C11  "C3'1"  "C2'1"    89.40  69.32  145  20.66   1.10  2.07  
2  13  C1  C11  "C3'1"  "C4'1"  -167.52  84.45  145  20.55  17.07  0.00  
#
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  17  0.915  0.246   1.179  
 2   2  22  0.875  0.183   0.043  
 3   3  22  0.929  0.132  -0.905  
 4   4  22  0.942  0.143  -0.701  
 5   5  23  0.920  0.138  -0.698  
 6   6  22  0.941  0.152  -0.533  
 7   7  22  0.937  0.143  -0.701  
 8   8  22  0.914  0.154  -0.496  
 9   9  22  0.909  0.240   1.102  
10  10  23  0.957  0.175   0.008  
11  11  16  0.948  0.133  -0.734  
12  12  20  0.949  0.153  -0.404  
13  13  41  0.916  0.174       ?  
14  14  20  0.968  0.162  -0.274  
15  15  19  0.967  0.142  -0.598  
16  16  20  0.958  0.154  -0.389  
17  17  20  0.972  0.179  -0.030  
18  18  20  0.972  0.165  -0.231  
19  19  22  0.888  0.189   0.266  
20  20   1  0.843  0.612       ?  
#
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        "1.8.4, CSD as541be (2020)"                                           Y  
3  eds          2.32.1                                                                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  
##
